Load Libraries

suppressMessages(library(minfi))
suppressMessages(library(reshape))
suppressMessages(library(ggplot2))
suppressMessages(library(gridExtra))
suppressMessages(library(RColorBrewer))
suppressMessages(library(here))
suppressMessages(library(binom))
suppressMessages(library(limma))
suppressMessages(library(sva))
suppressMessages(library(pamr))
suppressMessages(library(GEOquery))
suppressMessages(library(GEOmetadb))

suppressMessages(library(dplyr))
suppressMessages(library(lmtest))
suppressMessages(library(gridExtra))
suppressMessages(library(gtools))
suppressMessages(library(rafalib))


options(stringsAsFactors = FALSE)

Load Functions

source(here("scripts","00_pretty_plots.R"))
suppressMessages(source(here("scripts","00_heat_scree_plot_generic.R")))
source(here("scripts","00_EM_array_uniform_background_maximise_betabinom.R"))

Load Data

path<-"data/validation/DNAm"
epic.organoid1<-read.csv(here(path, "METH_K_Nayak_20035_SS_Plate1.csv"), skip=7)
epic.organoid1$plate_path<-paste(epic.organoid1$Sample_Plate,"_96_Samples",sep="")
epic.organoid2<-read.csv(here(path, "METH_K_Nayak_20035_SS_Plate2.csv"), skip=7)
epic.organoid2$plate_path<-paste(epic.organoid2$Sample_Plate,"_96_samples",sep="")
epic.organoid3<-read.csv(here(path, "METH_K_Nayak_20035_SS_Plate3.csv"), skip=7)
epic.organoid3$plate_path<-paste(epic.organoid3$Sample_Plate,"_16_samples",sep="")

epic.organoid<-rbind(epic.organoid1,epic.organoid2,epic.organoid3)

add gender

sampleInfo<-read.csv(here("data/validation", "Final samples for submission 2021.csv"))
epic.organoid<-merge(epic.organoid,sampleInfo[c("Sample.Name", "Age", "Diagnosis", "Gender", "GEPadGI", "BOX", "Segment","Source", "Wnt.type","Biobank.Rachel.Replicates")], by.x="Sample_Name", by.y="Sample.Name")

epic.organoid<-epic.organoid[which(epic.organoid$Biobank.Rachel.Replicates=="Rachel"),]

Normalize DNAm Arrays

here(path)
## [1] "/nfs/research1/zerbino/redgar/DNAm_organoid_passage/data/validation/DNAm"
epic.organoid$array.id.path <- file.path(here(path,"Data"),epic.organoid$plate_path, epic.organoid$Sentrix_ID, paste(epic.organoid$Sentrix_ID, epic.organoid$Sentrix_Position, sep="_"))
epic.organoid$array.id<-paste(epic.organoid$Sentrix_ID, epic.organoid$Sentrix_Position, sep="_")
epic.organoid$individual<-sapply(1:nrow(epic.organoid), function(x) strsplit(epic.organoid$Sample_Name[x]," ")[[1]][1])

epic.organoid$passage<-as.numeric(sapply(1:nrow(epic.organoid), function(x) gsub("p","",strsplit(epic.organoid$Sample_Name[x]," ")[[1]][3])))
epic.organoid$passage_hilo<-sapply(1:nrow(epic.organoid), function(x) if(epic.organoid$passage[x]<5){"low"}else{"high"})
epic.organoid$condition<-sapply(1:nrow(epic.organoid), function(x) strsplit(epic.organoid$Sample_Name[x]," ")[[1]][4])
epic.organoid$condition<-as.factor(epic.organoid$condition)
levels(epic.organoid$condition)<-c("D","IFNg","IFNg","TNFa","UD","UT")
epic.organoid$condition<-as.character(epic.organoid$condition)
epic.organoid$comparison<-sapply(1:nrow(epic.organoid), function(x) if(epic.organoid$condition[x]%in%c("UD","D")){"differentiation"}else{"cytokine"})
epic.organoid$treatment<-sapply(1:nrow(epic.organoid), function(x) if(epic.organoid$comparison[x]=="cytokine"){epic.organoid$condition[x]}else{"UT"})
epic.organoid$differentiation<-sapply(1:nrow(epic.organoid), function(x) if(epic.organoid$comparison[x]=="differentiation"){epic.organoid$condition[x]}else{"UD"})



# multiple DMAP files common with epic so need to force https://support.bioconductor.org/p/97773/
rgset_organoid <- read.metharray(epic.organoid$array.id.path, verbose = FALSE,force=TRUE)

# Background and dye bias correction with noob thhrough funnorm implemented in minfi
#http://bioconductor.org/help/course-materials/2015/BioC2015/methylation450k.html
MSet.illumina <- preprocessFunnorm(rgset_organoid, sex=epic.organoid$Gender)
## [preprocessFunnorm] Background and dye bias correction with noob
## Loading required package: IlluminaHumanMethylationEPICmanifest
## Loading required package: IlluminaHumanMethylationEPICanno.ilm10b4.hg19
## [preprocessFunnorm] Mapping to genome
## [preprocessFunnorm] Quantile extraction
## [preprocessFunnorm] Normalization
organoid_beta<-getBeta(MSet.illumina)

print(paste("Samples available: ",ncol(organoid_beta),"; Probes available: ",nrow(organoid_beta),sep=""))
## [1] "Samples available: 42; Probes available: 865859"

Detection p values across all probes for each sample

avg_detPval <- colMeans(detectionP(rgset_organoid))
epic.organoid$det_pval<-avg_detPval

ggplot(epic.organoid)+geom_boxplot(aes(as.factor(Sentrix_ID), det_pval, fill=as.factor(Sentrix_ID)), outlier.shape = NA)+
  geom_point(aes(as.factor(Sentrix_ID), det_pval, group=Sample_Name, fill=as.factor(Sentrix_ID)), shape=21, color="black",
             position = position_jitter(w = 0.25))+theme_bw()+theme(axis.text.x=element_text(angle = 45, vjust = 1, hjust=1))+
  xlab("Sentrix ID")+ylab("Mean Detection P Value")+guides(fill=FALSE)

ggsave(here("figs","validation_detection_pvalue_organoids.pdf"), width=6, height=5)
ggsave(here("figs/jpeg","validation_detection_pvalue_organoids.jpeg"), width=6, height=5)

Beta distribution before and after normalization

# extract raw beta values for plotting
beta_raw<-getBeta(rgset_organoid)
identical(colnames(beta_raw),epic.organoid$array.id)
## [1] TRUE
Beta_melted<- melt(organoid_beta)
Beta_melted_raw<- melt(beta_raw)

# Remove NAs before plotting (otherwise get many non-inifnite warnings)
Beta_Plot<-Beta_melted[which(!(is.na(Beta_melted$value))),]
Beta_Plot_raw<-Beta_melted_raw[which(!(is.na(Beta_melted_raw$value))),]

# Add meta data
colnames(Beta_Plot)<-c("CpG","ID","Beta")
Beta_Plot<-merge(Beta_Plot,epic.organoid, by.x="ID", by.y="array.id")
colnames(Beta_Plot_raw)<-c("CpG","ID","Beta")
Beta_Plot_raw<-merge(Beta_Plot_raw,epic.organoid, by.x="ID", by.y="array.id")

beta_dis_EPIC_raw<-ggplot(Beta_Plot_raw, aes(Beta, group=as.character(ID), color=as.character(Segment)))+
  geom_density()+theme_bw()+colscale_sampsite+xlab("DNAm Beta Value")

beta_dis_EPIC<-ggplot(Beta_Plot, aes(Beta, group=as.character(ID), color=as.character(Segment)))+
  geom_density()+theme_bw()+colscale_sampsite+xlab("DNAm Beta Value")


grid.arrange(beta_dis_EPIC_raw,beta_dis_EPIC)

ggsave(here("figs","validation_beta_distribution_organoid.pdf"),grid.arrange(beta_dis_EPIC_raw,beta_dis_EPIC),  w=10, h=5)
ggsave(here("figs/jpeg","validation_beta_distribution_organoid.jpeg"),grid.arrange(beta_dis_EPIC_raw,beta_dis_EPIC), w=10, h=5)

Confirm individuals ID with SNPs probes and clustering by DNAm

# remove rows with NAs
Betas_cluster<-organoid_beta[complete.cases(organoid_beta),]

d <- dist(t(Betas_cluster))
hc <- hclust(d, method = "complete") #single, complete, average, ward
myplclust(hc, labels=epic.organoid$Sample_Name, lab.col=as.fumeric(epic.organoid$Segment), cex=1.5)

pdf(here("figs","validation_cluster_wholeEPIC_organoid.pdf"), width=30)
myplclust(hc, labels=epic.organoid$Sample_Name, lab.col=as.fumeric(epic.organoid$Segment), cex=1.5)
dev.off()
## png 
##   2

Genotyping Probes

SNPs <- getSnpBeta(rgset_organoid)
SNPs<-SNPs[complete.cases(SNPs),]# 65 cause one was all NA

SNPs<-SNPs[,which(colnames(SNPs)%in%epic.organoid$array.id)]
identical(colnames(SNPs),epic.organoid$array.id)
## [1] TRUE
d <- dist(t(SNPs))
hc <- hclust(d, method = "complete") #single, complete, average, ward
myplclust(hc, labels=epic.organoid$Sample_Name, lab.col=as.fumeric(as.character(epic.organoid$individual)), cex=1.5)

pdf(here("figs","validation_cluster_snps_EPIC_organoid.pdf"), width=30)
myplclust(hc, labels=epic.organoid$Sample_Name, lab.col=as.fumeric(as.character(epic.organoid$individual)), cex=1.5)
dev.off()
## png 
##   2

Sex clustering

Using the cg ID to chromosome annotation from illumina https://emea.support.illumina.com/downloads/infinium-methylationepic-v1-0-product-files.html

anno_EPIC<-read.csv(here("data", "MethylationEPIC_v-1-0_B4.csv"), skip=7)

organoid_beta<-organoid_beta[which(rownames(organoid_beta)%in%anno_EPIC$IlmnID),]
anno_EPIC<-anno_EPIC[match(rownames(organoid_beta),anno_EPIC$IlmnID),]
identical(rownames(organoid_beta),anno_EPIC$IlmnID)
## [1] TRUE
organoid_beta_sex<-organoid_beta[which(anno_EPIC$CHR%in%c('X','Y')),]

d <- dist(t(organoid_beta_sex))
hc <- hclust(d, method = "complete") #single, complete, average, ward
myplclust(hc, labels=epic.organoid$Sample_Name, lab.col=as.fumeric(epic.organoid$Gender), cex=1.5)

pdf(here("figs","validation_cluster_sex_EPIC_organoid.pdf"), width=30)
myplclust(hc, labels=epic.organoid$Sample_Name, lab.col=as.fumeric(epic.organoid$Gender), cex=1.5)
dev.off()
## png 
##   2

Remove samples which do not cluster correctly

none to remove here though ### Probe Filtering

# SNP probes should already be removed
organoid_beta <- organoid_beta[!grepl("rs",rownames(organoid_beta)), ]
print(paste("Samples available: ",ncol(organoid_beta),"\nProbes available: ",nrow(organoid_beta),sep=""))
## [1] "Samples available: 42\nProbes available: 865859"

Sex Chromosomes

anno_EPIC<-anno_EPIC[anno_EPIC$IlmnID%in%rownames(organoid_beta),]
identical(rownames(organoid_beta),anno_EPIC$IlmnID)
## [1] TRUE
organoid_beta <- organoid_beta[!anno_EPIC$CHR%in%c("X", "Y"), ]

filt_sex<-nrow(organoid_beta)
print(paste("Samples available: ",ncol(organoid_beta),"\nProbes available: ",nrow(organoid_beta),sep=""))
## [1] "Samples available: 42\nProbes available: 846232"

Cross-hybridizing probes and polymorphic probes.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1066-1 “43,254 cross-reactive probes with ≥ 47 bp homology with an off-target site, of which 15,782 (36.5 %) are new to the EPIC platform” They include this annotated list in their supplement. wget https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM2_ESM.csv

cross_reactive<-read.csv(here("data", "13059_2016_1066_MOESM2_ESM.csv"), stringsAsFactors = F)
organoid_beta<-organoid_beta[which(!(rownames(organoid_beta)%in%cross_reactive$PROBE)),]

filt_cross<-nrow(organoid_beta)
print(paste("Samples available: ",ncol(organoid_beta),"\nProbes available: ",nrow(organoid_beta),sep=""))
## [1] "Samples available: 42\nProbes available: 814600"

For polymorphic probes I will The Pidsley annotation aswell for “Probes overlapping genetic variants at targeted CpG sites.” and “Probes overlapping genetic variants at single base extension sites for Infinium Type I probes” but NOT “Probes with genetic variants overlapping the body of the probe: 48 base pairs for Infinium Type I probes and 49 base pairs for Infinium Type II probes.”

#wget https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM4_ESM.csv
#wget https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM5_ESM.csv

polymorphic<-read.csv(here("data", "13059_2016_1066_MOESM4_ESM.csv"), stringsAsFactors = F)
print(paste("Filtering ",length(unique(polymorphic$PROBE))," polymorphic probes (genetic variants at targeted CpG sites).", sep=""))
## [1] "Filtering 12378 polymorphic probes (genetic variants at targeted CpG sites)."
baseext<-read.csv(here("data", "13059_2016_1066_MOESM5_ESM.csv"), stringsAsFactors = F)
print(paste("Filtering ",length(unique(baseext$PROBE))," polymorphic probes (single base extension sites for Infinium Type I probes).", sep=""))
## [1] "Filtering 413 polymorphic probes (single base extension sites for Infinium Type I probes)."
organoid_beta<-organoid_beta[which(!(rownames(organoid_beta)%in%c(polymorphic$PROBE, baseext$PROBE))),]

filt_poly<-nrow(organoid_beta)
print(paste("Samples available: ",ncol(organoid_beta),"\nProbes available: ",nrow(organoid_beta),sep=""))
## [1] "Samples available: 42\nProbes available: 802848"

Probe filtering based on detection pvalue and detection over background (NA)

Remove probes with high NA count

na_count_probe <-sapply(1:nrow(organoid_beta), function(y) length(which(is.na(organoid_beta[y,]))))
na_count_probe_good<-which(na_count_probe<(ncol(organoid_beta)*0.05))
organoid_beta<-organoid_beta[na_count_probe_good,]

filt_bead<-nrow(organoid_beta)
print(paste("Samples available: ",ncol(organoid_beta),"\nProbes available: ",nrow(organoid_beta),sep=""))
## [1] "Samples available: 42\nProbes available: 802848"

Remove probes with high detection p value across samples, and any samples with many high detection p value probes

detP <- detectionP(rgset_organoid)
detP<-detP[,which(colnames(detP)%in%epic.organoid$array.id)]
identical(colnames(detP),epic.organoid$array.id)
## [1] TRUE
failed <- detP>0.05
bad_det_p<-names(which(rowMeans(failed)>0.01))
bad_det_psamp<-names(which(colMeans(failed)>0.01))

organoid_beta<-organoid_beta[which(!(rownames(organoid_beta)%in%bad_det_p)),]
organoid_beta<-organoid_beta[,which(!(colnames(organoid_beta)%in%bad_det_psamp))]
identical(colnames(organoid_beta), as.character(epic.organoid$array.id))
## [1] TRUE
filt_detp<-nrow(organoid_beta)
print(paste("Samples available: ",ncol(organoid_beta),"\nProbes available: ",nrow(organoid_beta),sep=""))
## [1] "Samples available: 42\nProbes available: 801072"

Probe attrition plot

df<-data.frame(sample_num_remaining=c(866238,865918,865859,filt_sex,filt_cross,filt_poly,filt_bead,filt_detp),
               filter=c("EPIC Probe Number","Missing Annotation Data","Removal of SNP Probes",
                        "Removal of X and Y chromosome probes","Removal of Cross Reactive Probes",
                        "Removal of Polymorphic Probes", "Removal of Probes with Beadcount <3\nin 5 % of Samples",
                        "Removal of Probes with 1 % of samples\nwith a detection p-value greater than 0.05"))
df$sample_num_lost<-c(0,sapply(2:nrow(df), function(x) df$sample_num_remaining[x-1]-df$sample_num_remaining[x]))

df$filter<-factor(df$filter, rev(df$filter))

ggplot(df)+
  geom_bar(aes(filter,-sample_num_remaining), stat="identity", fill="grey70", color="black")+
  geom_bar(aes(filter,sample_num_lost), stat="identity",fill="darkred", color="black")+
  geom_text(aes(x=filter, y=-min(sample_num_remaining)/2,  label=comma(sample_num_remaining)))+
  geom_text(aes(x=filter, y=max(sample_num_lost)/1.5,  label=comma(sample_num_lost)))+
  geom_hline(yintercept=0)+
  coord_flip()+theme_bw()+ylab("")+xlab("")+
  theme(axis.line = element_blank(),
        axis.ticks = element_blank(),
        axis.text.x = element_blank(),
        axis.text.y = element_text(colour = "grey20", size=12),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(),
        panel.border = element_blank(),
        panel.background = element_blank()) +
  scale_x_discrete(position = "top")

ggsave(here("figs","validation_probe_attrition.pdf"), width = 8, height = 3)
ggsave(here("figs/jpeg","validation_probe_attrition.jpeg"), width = 8, height = 3)

epic.organoid<-epic.organoid[,which(!(colnames(epic.organoid)%in%c("array.id.path","plate_path","Biobank.Rachel.Replicates","GEPadGI","BOX","Source","Wnt.type","Sample_Group", "Pool_ID")))]

validation_organoid_beta<-organoid_beta
validation_epic.organoid<-epic.organoid

save(validation_organoid_beta, validation_epic.organoid, file=here("data/validation/DNAm","validation_betas_normalized.RData"))








load(file=here("data/validation/DNAm","validation_betas_normalized.RData"))

Principal Component Analysis (PCA)

pca_res <- prcomp(t(validation_organoid_beta))
Loadings<-as.data.frame(pca_res$x)
vars <- pca_res$sdev^2
Importance<-vars/sum(vars)

validation_epic.organoid$Sentrix_ID<-as.factor(as.character(validation_epic.organoid$Sentrix_ID))

meta_categorical <- validation_epic.organoid[, c(3,4, 8,9,11,13,16,17)]  # input column numbers in meta that contain categorical variables
meta_continuous <- as.data.frame(validation_epic.organoid[, c(6, 12,18)] ) # input column numbers in meta that contain continuous variables
colnames(meta_categorical) <- c("Plate","Sentrix ID","Gender","Segment","Individual", "passage_hilo", "treatment", "differentiation")
colnames(meta_continuous) <- c( "age","passage_numeric", "det_pval")

ord<-1:length(c(colnames(meta_categorical),colnames(meta_continuous)))
# how far do you want the plot to go?
PCs_to_view<-10

suppressWarnings(heat_scree_plot(Loadings, Importance, 3.3, 1.8))

ggsave(here("figs/validation_heat_scree.pdf"), suppressWarnings(heat_scree_plot(Loadings, Importance, 3.3, 1.8)),width = 9, height = 6)
ggsave(here("figs/jpeg","validation_heat_scree.jpeg"), suppressWarnings(heat_scree_plot(Loadings, Importance, 3.3, 1.8)),width = 9, height = 6)




## PC vs PC plot
Loadings$array.id<-rownames(Loadings)
Loadings_meta<-merge(Loadings, validation_epic.organoid, by="array.id")

ggplot(Loadings_meta, aes(PC1, PC2, fill=Segment))+geom_point(shape=21,size=3, color="black")+theme_bw()+
  xlab("PC1 (42%)")+ylab("PC2 (12%)")+th+theme(axis.text = element_text(size=12),
                                               axis.title = element_text(size=14),
                                               plot.margin = margin(1, 0.1, 1, 1, "cm"))+
  scale_fill_manual(values=c("#1a9850", "cornflowerblue","#e1e1ff","#1347a4","#000192"))

ggsave(here("figs","validation_PC12_site.pdf"), width = 5, height = 4)
ggsave(here("figs/jpeg","validation_PC12_site.jpeg"), width = 5, height = 4)




ggplot(Loadings_meta, aes(PC2, PC3, fill=passage_hilo))+
  geom_line(aes(PC2,PC3, group=individual, color=individual))+theme_bw()+
  geom_point(shape=21,size=3, color="black")+
  scale_color_manual(values=c("#d9d9d9","#525252","#969696","#737373","#bdbdbd"),name="Individual")+
  scale_fill_manual(values=c("#3288BD","#D53E4F"), name="Passage")+
  xlab("PC2 (12%)")+ylab("PC3 (11%)")+th+theme(axis.text = element_text(size=12),
                                               axis.title = element_text(size=14),
                                               plot.margin = margin(1, 1, 1, 1, "cm"))

ggsave(here("figs","validation_PC23_passage.pdf"), width = 5.5, height = 4)
ggsave(here("figs/jpeg","validation_PC23_passage.jpeg"), width = 5.5, height = 4)



ggplot(Loadings_meta, aes(PC2, PC3, fill=treatment, color=differentiation))+geom_point(shape=21,size=3)+
  scale_color_manual(values=c("black","white"))+scale_fill_manual(values=c("cornflowerblue","firebrick4","grey80"), name="Treatment")+
  theme_bw()+
  xlab("PC2 (12%)")+ylab("PC3 (11%)")+th+theme(axis.text = element_text(size=12),
                                               axis.title = element_text(size=14),
                                               plot.margin = margin(1, 1, 1, 1, "cm"))

ggsave(here("figs","validation_PC23_condition.pdf"), width = 6, height = 4)
ggsave(here("figs/jpeg","validation_PC23_condtion.jpeg"), width = 6, height = 4)

Overall Variance Across most Variable CpGs with Passage

Variation<-function(x) {quantile(x, c(0.9), na.rm=T)[[1]]-quantile(x, c(0.1), na.rm=T)[[1]]}
Mval<-function(beta) log2(beta/(1-beta))

organoid_mval = apply(validation_organoid_beta, 1, Mval)
organoid_mval = as.data.frame(organoid_mval)
organoid_mval = t(organoid_mval)

ref_range_dnam<-sapply(1:nrow(organoid_mval), function(x) Variation(organoid_mval[x,]))
validation_organoid_beta_VeryVariable<-validation_organoid_beta[which(ref_range_dnam>=2.75),]

print(paste("There are ",nrow(validation_organoid_beta_VeryVariable), " variable CpGs (10th-90th quantile range in M value >2.75)",sep=""))
## [1] "There are 26784 variable CpGs (10th-90th quantile range in M value >2.75)"
dim(validation_organoid_beta_VeryVariable<-validation_organoid_beta[rev(order(ref_range_dnam)),])
## [1] 801072     42

Include the same number of vairable CpGs as organoids varible. So take the 71384 most variable

dim(validation_organoid_beta_VeryVariable<-validation_organoid_beta_VeryVariable[1:71384 ,])
## [1] 71384    42
# beta plot variable CpGs
Beta_melted<- melt(validation_organoid_beta_VeryVariable)
Beta_Plot<-Beta_melted[which(!(is.na(Beta_melted$value))),]
colnames(Beta_Plot)<-c("CpG","ID","Beta")
Beta_Plot<-merge(Beta_Plot,validation_epic.organoid, by.x="ID", by.y="array.id")
Beta_Plot$passage.or.numeric.factor <- factor(Beta_Plot$passage, levels = c(12,9,8,4,3,2))

ggplot(Beta_Plot, aes(Beta,  color=passage.or.numeric.factor))+
  geom_density(size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
  scale_color_manual(values=rev(c("#D53E4F", "#F46D43", "#FEE08B", "#ABDDA4","#4CA5B1","#5E4FA2")), name="Passage\nNumber")

ggsave(here("figs/validation_variable_CpGs.pdf"),width = 3.75, height = 2.5)
ggsave(here("figs/jpeg","validation_variable_CpGs.jpeg"), width = 3.75, height = 2.5)


ggplot(Beta_Plot, aes(Beta,  color=passage.or.numeric.factor, group=ID))+
  geom_density(size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+facet_grid(condition~passage.or.numeric.factor)+
  scale_color_manual(values=rev(c("#D53E4F", "#F46D43", "#FEE08B", "#ABDDA4","#4CA5B1","#5E4FA2")), name="Passage\nNumber")

ggplot(Beta_Plot[which(Beta_Plot$differentiation=="UD" & Beta_Plot$treatment=="UT"),], aes(Beta,  color=passage.or.numeric.factor))+
  geom_density(size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
  scale_color_manual(values=rev(c("#D53E4F", "#F46D43", "#FEE08B", "#ABDDA4","#4CA5B1","#5E4FA2")), name="Passage\nNumber")

ggplot()+
  geom_density(aes(Beta,color=passage_hilo, group=ID),Beta_Plot, size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
  scale_color_manual(values = c ("#9ecae1", "#225ea8", "#081d58"), name="Relative\nPassage\nLevel within\nPatient")+facet_grid(condition~individual)+
  th+theme(strip.text = element_text(size = 10), axis.text=element_text(size=4),panel.spacing = unit(0.7, "lines"))+th+
  scale_x_continuous(breaks = c(0,0.5,1))

Beta_Plot$ID_nopass<-paste(Beta_Plot$individual, Beta_Plot$Segment,Beta_Plot$condition)
ggplot()+
  geom_density(aes(Beta,color=passage_hilo, group=ID),Beta_Plot, size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
  scale_color_manual(values = c ("#081d58","#9ecae1"), name="Relative\nPassage\nLevel within\nPatient")+facet_wrap(~ID_nopass)+
  th+theme(strip.text = element_text(size = 10), axis.text=element_text(size=4),panel.spacing = unit(0.7, "lines"))+th+
  scale_x_continuous(breaks = c(0,0.5,1))

ggsave(here("figs","validation_paired_beta.pdf"),width = 5, height = 2.2)
ggsave(here("figs/jpeg","validation_paired_beta.jpeg"),width = 10, height = 10)

ggplot()+
  geom_density(aes(Beta,color=passage.or.numeric.factor, group=ID),Beta_Plot, size=0.75)+theme_bw()+xlab("DNAm Beta Value")+ylab("Density")+
  scale_color_manual(values=rev(c("#D53E4F", "#F46D43", "#FEE08B", "#ABDDA4","#4CA5B1","#5E4FA2")))+facet_wrap(~ID_nopass)+
  th+theme(strip.text = element_text(size = 10), axis.text=element_text(size=4),panel.spacing = unit(0.7, "lines"))+th+
  scale_x_continuous(breaks = c(0,0.5,1))

Thresholding Trimodality

validation_epic.organoid$thresholded_prior_ratio<-sapply(1:nrow(validation_epic.organoid), function(x){
  print(x)
  converted<-as.numeric(round(validation_organoid_beta_VeryVariable[,x]*1000,0))
  counts<-rep(1000, length(converted))
  res = em(converted, counts, .41, .31, .27, 0.01, .1, .1, .90, .03, .5, .05)
  passage_threshold_params(converted, counts, res)
})
## [1] 1
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -397515.94       0.55       0.25       0.18       0.02       0.15
##  [7]       0.07       0.88       0.03       0.51       0.05
##  [1] -391627.52       0.58       0.24       0.16       0.02       0.15
##  [7]       0.07       0.87       0.03       0.52       0.04
##  [1] -391311.14       0.60       0.22       0.15       0.03       0.15
##  [7]       0.07       0.87       0.03       0.52       0.04
##  [1] -391271.60       0.61       0.22       0.14       0.04       0.15
##  [7]       0.06       0.87       0.03       0.52       0.04
##  [1] -391279.02       0.61       0.21       0.13       0.04       0.15
##  [7]       0.06       0.86       0.03       0.53       0.04
## [1] 2
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -397366.29       0.54       0.25       0.18       0.02       0.15
##  [7]       0.07       0.88       0.03       0.51       0.05
##  [1] -391640.40       0.58       0.24       0.16       0.02       0.15
##  [7]       0.07       0.87       0.03       0.51       0.04
##  [1] -391333.52       0.60       0.23       0.15       0.03       0.15
##  [7]       0.07       0.87       0.03       0.52       0.04
##  [1] -391300.52       0.61       0.22       0.14       0.04       0.15
##  [7]       0.06       0.87       0.03       0.52       0.04
##  [1] -391314.51       0.61       0.21       0.14       0.04       0.15
##  [7]       0.06       0.87       0.03       0.53       0.04
##  [1] -391337.56       0.61       0.21       0.14       0.05       0.14
##  [7]       0.06       0.87       0.03       0.53       0.04
##  [1] -391359.52       0.61       0.20       0.13       0.05       0.14
##  [7]       0.06       0.87       0.03       0.53       0.04
##  [1] -391372.26       0.61       0.20       0.13       0.06       0.14
##  [7]       0.05       0.87       0.03       0.53       0.04
##  [1] -391373.64       0.61       0.20       0.13       0.06       0.14
##  [7]       0.05       0.87       0.03       0.53       0.04
## [1] 3
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -399244.49       0.56       0.23       0.19       0.02       0.15
##  [7]       0.08       0.88       0.03       0.51       0.05
##  [1] -392243.87       0.59       0.21       0.17       0.02       0.16
##  [7]       0.07       0.87       0.03       0.52       0.05
##  [1] -391647.41       0.61       0.20       0.16       0.03       0.17
##  [7]       0.07       0.86       0.03       0.53       0.04
##  [1] -391483.96       0.62       0.19       0.16       0.03       0.17
##  [7]       0.07       0.86       0.03       0.53       0.04
##  [1] -391420.21       0.62       0.18       0.16       0.04       0.17
##  [7]       0.07       0.86       0.03       0.54       0.04
##  [1] -391392.00       0.62       0.18       0.16       0.04       0.17
##  [7]       0.07       0.85       0.03       0.54       0.04
##  [1] -391379.20       0.62       0.17       0.16       0.05       0.17
##  [7]       0.07       0.85       0.03       0.54       0.04
##  [1] -391372.70       0.62       0.17       0.16       0.05       0.16
##  [7]       0.07       0.85       0.03       0.55       0.04
## [1] 4
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -398551.07       0.55       0.23       0.20       0.02       0.15
##  [7]       0.07       0.88       0.03       0.51       0.05
##  [1] -392065.62       0.59       0.21       0.18       0.02       0.16
##  [7]       0.07       0.87       0.03       0.52       0.04
##  [1] -391596.77       0.61       0.19       0.17       0.03       0.17
##  [7]       0.07       0.87       0.03       0.52       0.04
##  [1] -391474.81       0.62       0.19       0.16       0.04       0.17
##  [7]       0.07       0.86       0.03       0.53       0.04
##  [1] -391423.89       0.62       0.18       0.16       0.04       0.17
##  [7]       0.07       0.86       0.03       0.54       0.04
##  [1] -391395.66       0.62       0.18       0.16       0.04       0.17
##  [7]       0.07       0.86       0.03       0.54       0.04
##  [1] -391376.19       0.62       0.17       0.16       0.05       0.17
##  [7]       0.07       0.86       0.03       0.54       0.04
##  [1] -391359.68       0.62       0.17       0.16       0.05       0.16
##  [7]       0.07       0.86       0.03       0.55       0.04
##  [1] -391343.96       0.62       0.17       0.16       0.06       0.16
##  [7]       0.07       0.86       0.03       0.55       0.04
##  [1] -391325.61       0.61       0.17       0.16       0.06       0.16
##  [7]       0.06       0.86       0.03       0.55       0.04
##  [1] -391303.71       0.61       0.17       0.16       0.07       0.16
##  [7]       0.06       0.86       0.03       0.55       0.04
##  [1] -391277.80       0.60       0.17       0.16       0.07       0.16
##  [7]       0.06       0.86       0.03       0.55       0.05
##  [1] -391247.99       0.60       0.17       0.16       0.08       0.16
##  [7]       0.06       0.86       0.03       0.55       0.05
##  [1] -391214.76       0.59       0.17       0.16       0.08       0.16
##  [7]       0.06       0.86       0.03       0.56       0.05
##  [1] -391178.90       0.59       0.17       0.16       0.08       0.16
##  [7]       0.06       0.86       0.03       0.56       0.05
##  [1] -391141.28       0.58       0.17       0.16       0.09       0.15
##  [7]       0.06       0.87       0.03       0.56       0.05
##  [1] -391102.71       0.58       0.17       0.16       0.09       0.15
##  [7]       0.06       0.87       0.03       0.56       0.05
##  [1] -391064.15       0.57       0.17       0.16       0.10       0.15
##  [7]       0.06       0.87       0.03       0.56       0.05
##  [1] -391026.39       0.57       0.18       0.16       0.10       0.15
##  [7]       0.06       0.87       0.03       0.56       0.06
##  [1] -390990.11       0.56       0.18       0.16       0.10       0.15
##  [7]       0.06       0.87       0.03       0.56       0.06
##  [1] -390955.86       0.56       0.18       0.16       0.11       0.15
##  [7]       0.06       0.87       0.03       0.56       0.06
##  [1] -390924.08       0.55       0.18       0.16       0.11       0.15
##  [7]       0.06       0.87       0.03       0.56       0.06
##  [1] -390895.07       0.55       0.18       0.16       0.12       0.15
##  [7]       0.06       0.87       0.03       0.56       0.06
##  [1] -390869.01       0.54       0.18       0.16       0.12       0.15
##  [7]       0.06       0.87       0.03       0.56       0.07
##  [1] -390846.05       0.53       0.18       0.16       0.12       0.15
##  [7]       0.06       0.87       0.03       0.56       0.07
##  [1] -390826.23       0.53       0.18       0.16       0.13       0.15
##  [7]       0.06       0.87       0.03       0.56       0.07
##  [1] -390809.51       0.52       0.18       0.16       0.13       0.15
##  [7]       0.06       0.87       0.03       0.56       0.07
##  [1] -390795.83       0.52       0.18       0.16       0.14       0.15
##  [7]       0.05       0.87       0.03       0.56       0.07
##  [1] -390785.07       0.51       0.19       0.16       0.14       0.15
##  [7]       0.05       0.87       0.03       0.56       0.08
##  [1] -390777.10       0.50       0.19       0.16       0.15       0.15
##  [7]       0.05       0.87       0.03       0.56       0.08
## [1] 5
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -401736.10       0.57       0.26       0.15       0.02       0.15
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393400.10       0.61       0.24       0.12       0.03       0.16
##  [7]       0.07       0.85       0.03       0.52       0.05
##  [1] -392470.87       0.62       0.23       0.11       0.03       0.16
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392163.86       0.63       0.23       0.11       0.04       0.16
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392045.42       0.63       0.22       0.10       0.04       0.16
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392005.88       0.63       0.22       0.10       0.05       0.16
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391999.88       0.63       0.22       0.10       0.05       0.16
##  [7]       0.06       0.82       0.04       0.54       0.04
## [1] 6
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403181.16       0.59       0.25       0.14       0.02       0.16
##  [7]       0.07       0.86       0.03       0.51       0.05
##  [1] -393624.52       0.62       0.24       0.11       0.03       0.17
##  [7]       0.07       0.85       0.03       0.52       0.04
##  [1] -392548.39       0.64       0.23       0.10       0.03       0.17
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392184.71       0.64       0.22       0.09       0.04       0.17
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392038.21       0.64       0.22       0.09       0.05       0.17
##  [7]       0.07       0.82       0.04       0.53       0.04
##  [1] -391983.60       0.64       0.22       0.09       0.05       0.17
##  [7]       0.06       0.82       0.04       0.53       0.04
##  [1] -391969.28       0.63       0.22       0.09       0.06       0.17
##  [7]       0.06       0.81       0.04       0.54       0.04
##  [1] -391968.67       0.62       0.22       0.09       0.07       0.17
##  [7]       0.06       0.81       0.04       0.54       0.04
## [1] 7
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -404190.72       0.60       0.24       0.14       0.02       0.16
##  [7]       0.07       0.86       0.03       0.51       0.05
##  [1] -393891.24       0.64       0.22       0.11       0.03       0.17
##  [7]       0.07       0.84       0.03       0.52       0.04
##  [1] -392563.39       0.65       0.21       0.11       0.04       0.18
##  [7]       0.07       0.83       0.03       0.53       0.04
##  [1] -392120.86       0.65       0.20       0.10       0.04       0.18
##  [7]       0.07       0.82       0.03       0.53       0.04
##  [1] -391966.08       0.65       0.20       0.10       0.05       0.18
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -391933.91       0.64       0.20       0.10       0.06       0.18
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -391953.46       0.64       0.20       0.10       0.06       0.18
##  [7]       0.07       0.80       0.04       0.54       0.04
##  [1] -391988.49       0.63       0.20       0.11       0.07       0.18
##  [7]       0.07       0.80       0.04       0.55       0.04
##  [1] -392018.66       0.62       0.20       0.11       0.08       0.18
##  [7]       0.07       0.80       0.04       0.55       0.04
##  [1] -392034.98       0.61       0.20       0.11       0.08       0.18
##  [7]       0.07       0.79       0.04       0.55       0.04
##  [1] -392034.36       0.59       0.21       0.11       0.09       0.18
##  [7]       0.07       0.79       0.04       0.55       0.04
## [1] 8
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -402715.66       0.58       0.24       0.15       0.02       0.16
##  [7]       0.07       0.86       0.03       0.51       0.05
##  [1] -393422.88       0.62       0.23       0.13       0.03       0.17
##  [7]       0.07       0.85       0.03       0.52       0.05
##  [1] -392383.64       0.63       0.22       0.12       0.03       0.17
##  [7]       0.07       0.84       0.03       0.53       0.04
##  [1] -392049.59       0.64       0.21       0.12       0.04       0.18
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -391925.07       0.64       0.20       0.12       0.04       0.18
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391886.99       0.63       0.20       0.12       0.05       0.18
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -391886.54       0.63       0.20       0.12       0.05       0.18
##  [7]       0.07       0.82       0.04       0.54       0.04
## [1] 9
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -401261.69       0.58       0.21       0.19       0.02       0.16
##  [7]       0.08       0.87       0.03       0.51       0.05
##  [1] -392806.79       0.62       0.18       0.17       0.03       0.18
##  [7]       0.08       0.86       0.03       0.52       0.04
##  [1] -391920.67       0.64       0.17       0.16       0.03       0.19
##  [7]       0.08       0.85       0.03       0.53       0.04
##  [1] -391632.83       0.65       0.16       0.16       0.04       0.19
##  [7]       0.08       0.85       0.03       0.54       0.04
##  [1] -391502.84       0.65       0.15       0.15       0.05       0.19
##  [7]       0.08       0.84       0.03       0.54       0.04
##  [1] -391434.58       0.64       0.15       0.15       0.06       0.19
##  [7]       0.08       0.84       0.03       0.55       0.04
##  [1] -391394.46       0.64       0.14       0.16       0.06       0.20
##  [7]       0.08       0.84       0.03       0.55       0.04
##  [1] -391367.24       0.63       0.14       0.16       0.07       0.20
##  [7]       0.08       0.84       0.03       0.55       0.04
##  [1] -391345.65       0.62       0.14       0.16       0.07       0.19
##  [7]       0.08       0.84       0.03       0.55       0.04
##  [1] -391324.99       0.62       0.15       0.16       0.08       0.19
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391303.07       0.61       0.15       0.16       0.08       0.19
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391279.08       0.60       0.15       0.16       0.09       0.19
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391252.94       0.59       0.15       0.16       0.09       0.19
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391224.95       0.58       0.15       0.17       0.10       0.19
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391195.57       0.57       0.16       0.17       0.10       0.19
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391165.37       0.56       0.16       0.17       0.11       0.19
##  [7]       0.08       0.84       0.04       0.56       0.05
##  [1] -391134.91       0.55       0.16       0.17       0.11       0.19
##  [7]       0.08       0.84       0.04       0.56       0.05
##  [1] -391105.88       0.54       0.16       0.17       0.12       0.19
##  [7]       0.08       0.84       0.04       0.56       0.05
##  [1] -391075.56       0.54       0.17       0.17       0.12       0.19
##  [7]       0.08       0.84       0.04       0.56       0.05
##  [1] -391046.95       0.53       0.17       0.18       0.13       0.19
##  [7]       0.08       0.84       0.04       0.56       0.05
##  [1] -391020.14       0.52       0.17       0.18       0.13       0.19
##  [7]       0.08       0.84       0.04       0.56       0.05
##  [1] -390995.03       0.51       0.18       0.18       0.14       0.19
##  [7]       0.08       0.84       0.04       0.56       0.05
##  [1] -390971.85       0.50       0.18       0.18       0.14       0.19
##  [7]       0.08       0.84       0.03       0.56       0.05
##  [1] -390950.61       0.49       0.18       0.18       0.15       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
##  [1] -390931.35       0.48       0.18       0.18       0.15       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
##  [1] -390914.09       0.47       0.19       0.18       0.16       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
##  [1] -390898.81       0.46       0.19       0.19       0.16       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
##  [1] -390885.44       0.45       0.19       0.19       0.17       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
##  [1] -390873.91       0.44       0.19       0.19       0.17       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
##  [1] -390863.90       0.44       0.20       0.19       0.18       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
##  [1] -390855.79       0.43       0.20       0.19       0.18       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
## [1] 10
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -400720.44       0.58       0.20       0.20       0.02       0.17
##  [7]       0.08       0.87       0.03       0.51       0.05
##  [1] -392763.80       0.62       0.17       0.18       0.03       0.19
##  [7]       0.08       0.87       0.03       0.52       0.04
##  [1] -391942.07       0.64       0.15       0.17       0.04       0.20
##  [7]       0.08       0.86       0.03       0.53       0.04
##  [1] -391656.08       0.65       0.15       0.16       0.04       0.20
##  [7]       0.08       0.86       0.03       0.53       0.04
##  [1] -391516.99       0.65       0.14       0.16       0.05       0.21
##  [7]       0.08       0.85       0.04       0.54       0.04
##  [1] -391436.11       0.65       0.14       0.16       0.06       0.21
##  [7]       0.08       0.85       0.04       0.55       0.04
##  [1] -391381.68       0.64       0.13       0.16       0.06       0.21
##  [7]       0.08       0.85       0.04       0.55       0.04
##  [1] -391339.68       0.63       0.13       0.16       0.07       0.21
##  [7]       0.08       0.85       0.04       0.55       0.04
##  [1] -391303.39       0.63       0.13       0.17       0.07       0.21
##  [7]       0.08       0.85       0.04       0.56       0.04
##  [1] -391270.19       0.62       0.14       0.17       0.08       0.21
##  [7]       0.08       0.85       0.04       0.56       0.04
##  [1] -391237.85       0.61       0.14       0.17       0.08       0.21
##  [7]       0.08       0.85       0.04       0.56       0.04
##  [1] -391205.97       0.60       0.14       0.17       0.09       0.21
##  [7]       0.08       0.85       0.04       0.56       0.04
##  [1] -391174.14       0.59       0.14       0.17       0.09       0.21
##  [7]       0.08       0.85       0.04       0.56       0.04
##  [1] -391143.01       0.59       0.14       0.17       0.10       0.21
##  [7]       0.08       0.85       0.04       0.56       0.04
##  [1] -391112.14       0.58       0.15       0.17       0.10       0.21
##  [7]       0.08       0.85       0.04       0.57       0.04
##  [1] -391082.01       0.57       0.15       0.18       0.11       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -391052.94       0.56       0.15       0.18       0.11       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -391025.10       0.55       0.16       0.18       0.12       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390998.66       0.54       0.16       0.18       0.12       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390973.70       0.53       0.16       0.18       0.13       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390950.37       0.52       0.16       0.18       0.13       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390928.73       0.51       0.17       0.18       0.14       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390908.84       0.51       0.17       0.18       0.14       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390890.72       0.50       0.17       0.19       0.15       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390874.38       0.49       0.18       0.19       0.15       0.21
##  [7]       0.08       0.85       0.04       0.57       0.06
##  [1] -390859.78       0.48       0.18       0.19       0.15       0.21
##  [7]       0.08       0.86       0.04       0.57       0.06
##  [1] -390846.90       0.47       0.18       0.19       0.16       0.21
##  [7]       0.08       0.86       0.04       0.57       0.06
##  [1] -390835.69       0.46       0.18       0.19       0.17       0.21
##  [7]       0.08       0.86       0.04       0.57       0.06
##  [1] -390826.09       0.45       0.19       0.19       0.17       0.21
##  [7]       0.08       0.86       0.03       0.57       0.06
## [1] 11
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -400291.39       0.57       0.23       0.19       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -392644.37       0.61       0.21       0.16       0.03       0.17
##  [7]       0.07       0.87       0.03       0.52       0.04
##  [1] -392023.33       0.62       0.19       0.15       0.03       0.18
##  [7]       0.07       0.86       0.03       0.52       0.04
##  [1] -391857.40       0.63       0.19       0.15       0.04       0.18
##  [7]       0.07       0.86       0.03       0.53       0.04
##  [1] -391790.60       0.63       0.18       0.14       0.04       0.18
##  [7]       0.07       0.85       0.03       0.53       0.04
##  [1] -391754.53       0.63       0.18       0.14       0.05       0.18
##  [7]       0.07       0.85       0.04       0.53       0.04
##  [1] -391728.88       0.63       0.18       0.14       0.05       0.18
##  [7]       0.07       0.85       0.04       0.54       0.04
##  [1] -391705.90       0.62       0.17       0.14       0.06       0.18
##  [7]       0.07       0.85       0.04       0.54       0.04
##  [1] -391682.67       0.62       0.17       0.14       0.06       0.18
##  [7]       0.07       0.85       0.04       0.54       0.04
##  [1] -391656.61       0.61       0.17       0.15       0.07       0.18
##  [7]       0.07       0.85       0.04       0.54       0.04
##  [1] -391627.05       0.61       0.18       0.15       0.07       0.18
##  [7]       0.07       0.85       0.04       0.54       0.04
##  [1] -391594.02       0.60       0.18       0.15       0.08       0.18
##  [7]       0.07       0.85       0.04       0.55       0.04
##  [1] -391557.97       0.59       0.18       0.15       0.08       0.17
##  [7]       0.07       0.85       0.04       0.55       0.04
##  [1] -391519.20       0.59       0.18       0.15       0.08       0.17
##  [7]       0.06       0.85       0.04       0.55       0.05
##  [1] -391478.70       0.58       0.18       0.15       0.09       0.17
##  [7]       0.06       0.85       0.04       0.55       0.05
##  [1] -391436.85       0.57       0.18       0.15       0.09       0.17
##  [7]       0.06       0.85       0.04       0.55       0.05
##  [1] -391395.22       0.57       0.18       0.15       0.10       0.17
##  [7]       0.06       0.85       0.04       0.55       0.05
##  [1] -391353.56       0.56       0.18       0.16       0.10       0.17
##  [7]       0.06       0.85       0.04       0.55       0.05
##  [1] -391313.67       0.55       0.19       0.16       0.11       0.17
##  [7]       0.06       0.85       0.04       0.55       0.05
##  [1] -391275.93       0.54       0.19       0.16       0.11       0.17
##  [7]       0.06       0.85       0.04       0.55       0.05
##  [1] -391240.19       0.54       0.19       0.16       0.11       0.17
##  [7]       0.06       0.85       0.04       0.55       0.06
##  [1] -391206.76       0.53       0.19       0.16       0.12       0.17
##  [7]       0.06       0.85       0.04       0.55       0.06
##  [1] -391175.85       0.52       0.19       0.16       0.12       0.17
##  [7]       0.06       0.85       0.04       0.54       0.06
##  [1] -391147.56       0.51       0.20       0.16       0.13       0.17
##  [7]       0.06       0.85       0.04       0.54       0.06
##  [1] -391121.90       0.51       0.20       0.16       0.13       0.17
##  [7]       0.06       0.85       0.04       0.54       0.06
##  [1] -391098.86       0.50       0.20       0.16       0.14       0.17
##  [7]       0.06       0.85       0.04       0.54       0.06
##  [1] -391078.34       0.49       0.20       0.17       0.14       0.17
##  [7]       0.06       0.85       0.04       0.54       0.06
##  [1] -391058.86       0.48       0.20       0.17       0.15       0.17
##  [7]       0.06       0.85       0.04       0.54       0.07
##  [1] -391042.37       0.48       0.20       0.17       0.15       0.17
##  [7]       0.06       0.85       0.04       0.54       0.07
##  [1] -391028.36       0.47       0.21       0.17       0.16       0.17
##  [7]       0.06       0.85       0.04       0.54       0.07
##  [1] -391016.45       0.46       0.21       0.17       0.16       0.17
##  [7]       0.06       0.85       0.04       0.54       0.07
##  [1] -391004.70       0.45       0.21       0.17       0.17       0.17
##  [7]       0.06       0.85       0.04       0.54       0.07
##  [1] -390996.07       0.45       0.21       0.17       0.17       0.17
##  [7]       0.06       0.86       0.04       0.54       0.07
## [1] 12
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -400398.93       0.58       0.22       0.18       0.02       0.16
##  [7]       0.08       0.87       0.03       0.51       0.05
##  [1] -392994.09       0.61       0.20       0.16       0.03       0.17
##  [7]       0.08       0.86       0.03       0.52       0.04
##  [1] -392346.60       0.63       0.19       0.15       0.03       0.18
##  [7]       0.08       0.86       0.03       0.52       0.04
##  [1] -392164.50       0.64       0.18       0.14       0.04       0.18
##  [7]       0.08       0.85       0.03       0.53       0.04
##  [1] -392090.16       0.64       0.17       0.14       0.05       0.18
##  [7]       0.08       0.85       0.03       0.53       0.04
##  [1] -392050.33       0.64       0.17       0.14       0.05       0.19
##  [7]       0.08       0.85       0.04       0.54       0.04
##  [1] -392022.23       0.64       0.17       0.14       0.06       0.19
##  [7]       0.08       0.85       0.04       0.54       0.04
##  [1] -391997.27       0.63       0.17       0.14       0.06       0.18
##  [7]       0.08       0.85       0.04       0.54       0.04
##  [1] -391972.55       0.63       0.17       0.14       0.07       0.18
##  [7]       0.08       0.85       0.04       0.54       0.04
##  [1] -391945.82       0.62       0.17       0.14       0.07       0.18
##  [7]       0.08       0.85       0.04       0.54       0.04
##  [1] -391916.61       0.61       0.17       0.14       0.08       0.18
##  [7]       0.08       0.85       0.04       0.55       0.04
##  [1] -391884.90       0.61       0.17       0.14       0.08       0.18
##  [7]       0.08       0.85       0.04       0.55       0.04
##  [1] -391851.37       0.60       0.17       0.14       0.09       0.18
##  [7]       0.07       0.85       0.04       0.55       0.04
##  [1] -391815.84       0.59       0.17       0.15       0.09       0.18
##  [7]       0.07       0.85       0.04       0.55       0.04
##  [1] -391779.28       0.58       0.17       0.15       0.09       0.18
##  [7]       0.07       0.85       0.04       0.55       0.04
##  [1] -391741.62       0.58       0.18       0.15       0.10       0.18
##  [7]       0.07       0.85       0.04       0.55       0.05
##  [1] -391704.48       0.57       0.18       0.15       0.10       0.18
##  [7]       0.07       0.85       0.04       0.55       0.05
##  [1] -391666.96       0.56       0.18       0.15       0.11       0.18
##  [7]       0.07       0.85       0.04       0.55       0.05
##  [1] -391631.57       0.55       0.18       0.15       0.11       0.18
##  [7]       0.07       0.85       0.04       0.55       0.05
##  [1] -391598.07       0.55       0.18       0.15       0.12       0.18
##  [7]       0.07       0.85       0.04       0.55       0.05
##  [1] -391566.28       0.54       0.19       0.15       0.12       0.18
##  [7]       0.07       0.85       0.04       0.55       0.05
##  [1] -391536.59       0.53       0.19       0.16       0.13       0.18
##  [7]       0.07       0.85       0.04       0.55       0.05
##  [1] -391509.12       0.52       0.19       0.16       0.13       0.18
##  [7]       0.07       0.85       0.04       0.55       0.06
##  [1] -391483.96       0.52       0.19       0.16       0.13       0.17
##  [7]       0.07       0.85       0.04       0.55       0.06
##  [1] -391461.14       0.51       0.19       0.16       0.14       0.17
##  [7]       0.07       0.85       0.04       0.55       0.06
##  [1] -391440.66       0.50       0.20       0.16       0.14       0.17
##  [7]       0.07       0.85       0.04       0.55       0.06
##  [1] -391422.48       0.49       0.20       0.16       0.15       0.17
##  [7]       0.07       0.85       0.04       0.55       0.06
##  [1] -391406.56       0.48       0.20       0.16       0.15       0.17
##  [7]       0.07       0.85       0.04       0.55       0.06
##  [1] -391392.80       0.48       0.20       0.16       0.16       0.17
##  [7]       0.07       0.85       0.04       0.55       0.06
##  [1] -391381.12       0.47       0.20       0.17       0.16       0.17
##  [7]       0.07       0.85       0.04       0.55       0.07
##  [1] -391371.06       0.46       0.20       0.17       0.17       0.17
##  [7]       0.07       0.85       0.04       0.55       0.07
##  [1] -391360.75       0.45       0.21       0.17       0.17       0.17
##  [7]       0.07       0.85       0.04       0.54       0.07
##  [1] -391353.90       0.44       0.21       0.17       0.18       0.17
##  [7]       0.07       0.85       0.04       0.54       0.07
## [1] 13
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403138.89       0.59       0.23       0.16       0.02       0.16
##  [7]       0.08       0.86       0.03       0.51       0.05
##  [1] -393726.11       0.63       0.20       0.14       0.03       0.17
##  [7]       0.08       0.85       0.03       0.52       0.05
##  [1] -392454.83       0.65       0.19       0.13       0.03       0.18
##  [7]       0.08       0.83       0.03       0.53       0.04
##  [1] -392029.12       0.65       0.18       0.13       0.04       0.18
##  [7]       0.08       0.83       0.04       0.54       0.04
##  [1] -391881.03       0.65       0.18       0.13       0.05       0.18
##  [7]       0.08       0.82       0.04       0.54       0.04
##  [1] -391849.05       0.65       0.17       0.13       0.05       0.18
##  [7]       0.08       0.82       0.04       0.54       0.04
##  [1] -391863.32       0.64       0.17       0.13       0.06       0.18
##  [7]       0.08       0.81       0.04       0.55       0.04
##  [1] -391889.93       0.63       0.17       0.13       0.06       0.18
##  [7]       0.07       0.81       0.04       0.55       0.04
##  [1] -391911.78       0.62       0.17       0.13       0.07       0.18
##  [7]       0.07       0.81       0.04       0.55       0.04
##  [1] -391921.40       0.61       0.17       0.14       0.07       0.18
##  [7]       0.07       0.81       0.04       0.55       0.04
## [1] 14
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403611.87       0.60       0.22       0.16       0.02       0.16
##  [7]       0.08       0.86       0.03       0.51       0.05
##  [1] -393996.17       0.64       0.20       0.13       0.03       0.18
##  [7]       0.08       0.85       0.03       0.52       0.04
##  [1] -392661.94       0.65       0.19       0.12       0.04       0.18
##  [7]       0.08       0.83       0.04       0.53       0.04
##  [1] -392206.40       0.66       0.18       0.12       0.04       0.19
##  [7]       0.08       0.83       0.04       0.53       0.04
##  [1] -392045.57       0.66       0.17       0.12       0.05       0.19
##  [7]       0.08       0.82       0.04       0.54       0.04
##  [1] -392008.21       0.65       0.17       0.12       0.06       0.19
##  [7]       0.08       0.81       0.04       0.54       0.04
##  [1] -392020.53       0.64       0.17       0.12       0.06       0.19
##  [7]       0.08       0.81       0.04       0.54       0.04
##  [1] -392046.43       0.64       0.17       0.13       0.07       0.19
##  [7]       0.08       0.81       0.04       0.55       0.04
##  [1] -392067.83       0.63       0.17       0.13       0.07       0.19
##  [7]       0.08       0.80       0.04       0.55       0.04
##  [1] -392077.62       0.62       0.17       0.13       0.08       0.19
##  [7]       0.08       0.80       0.04       0.55       0.04
## [1] 15
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403588.34       0.60       0.24       0.14       0.02       0.16
##  [7]       0.08       0.86       0.03       0.51       0.05
##  [1] -394220.97       0.64       0.22       0.12       0.03       0.18
##  [7]       0.08       0.85       0.03       0.52       0.04
##  [1] -393021.13       0.65       0.20       0.11       0.04       0.18
##  [7]       0.08       0.83       0.04       0.52       0.04
##  [1] -392593.88       0.66       0.20       0.10       0.04       0.19
##  [7]       0.08       0.83       0.04       0.53       0.04
##  [1] -392423.11       0.66       0.19       0.10       0.05       0.19
##  [7]       0.08       0.82       0.04       0.53       0.04
##  [1] -392365.42       0.65       0.19       0.10       0.06       0.19
##  [7]       0.08       0.81       0.04       0.54       0.04
##  [1] -392358.77       0.65       0.19       0.10       0.06       0.19
##  [7]       0.08       0.81       0.04       0.54       0.04
## [1] 16
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403501.55       0.60       0.23       0.15       0.02       0.16
##  [7]       0.08       0.86       0.03       0.51       0.05
##  [1] -394218.47       0.64       0.21       0.12       0.03       0.18
##  [7]       0.08       0.85       0.03       0.52       0.04
##  [1] -393033.25       0.65       0.20       0.11       0.04       0.19
##  [7]       0.08       0.84       0.04       0.52       0.04
##  [1] -392617.32       0.66       0.19       0.10       0.04       0.19
##  [7]       0.08       0.83       0.04       0.53       0.04
##  [1] -392452.85       0.66       0.19       0.10       0.05       0.19
##  [7]       0.08       0.82       0.04       0.53       0.04
##  [1] -392398.02       0.65       0.19       0.10       0.06       0.19
##  [7]       0.08       0.82       0.04       0.54       0.04
##  [1] -392392.35       0.65       0.19       0.10       0.06       0.19
##  [7]       0.08       0.81       0.04       0.54       0.04
## [1] 17
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -399928.06       0.57       0.19       0.22       0.02       0.16
##  [7]       0.09       0.87       0.03       0.51       0.05
##  [1] -392356.74       0.61       0.15       0.21       0.03       0.18
##  [7]       0.09       0.86       0.03       0.53       0.05
##  [1] -391316.08       0.63       0.14       0.20       0.03       0.19
##  [7]       0.09       0.85       0.03       0.54       0.04
##  [1] -390938.56       0.63       0.12       0.20       0.04       0.20
##  [7]       0.10       0.85       0.03       0.54       0.04
##  [1] -390775.20       0.63       0.12       0.20       0.04       0.20
##  [7]       0.10       0.85       0.03       0.55       0.04
##  [1] -390704.67       0.63       0.11       0.21       0.05       0.20
##  [7]       0.10       0.84       0.04       0.56       0.04
##  [1] -390676.38       0.63       0.11       0.21       0.05       0.21
##  [7]       0.10       0.84       0.04       0.56       0.04
##  [1] -390665.19       0.62       0.11       0.21       0.06       0.21
##  [7]       0.10       0.84       0.04       0.56       0.04
##  [1] -390658.34       0.61       0.11       0.21       0.06       0.21
##  [7]       0.10       0.84       0.04       0.56       0.04
## [1] 18
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -398969.63       0.57       0.18       0.23       0.02       0.16
##  [7]       0.09       0.87       0.03       0.51       0.05
##  [1] -392350.42       0.61       0.15       0.22       0.03       0.18
##  [7]       0.09       0.86       0.03       0.53       0.04
##  [1] -391393.38       0.63       0.13       0.21       0.03       0.19
##  [7]       0.10       0.86       0.03       0.54       0.04
##  [1] -391026.20       0.63       0.12       0.21       0.04       0.20
##  [7]       0.10       0.85       0.03       0.54       0.04
##  [1] -390857.04       0.63       0.11       0.21       0.04       0.20
##  [7]       0.11       0.85       0.04       0.55       0.04
##  [1] -390775.81       0.63       0.11       0.21       0.05       0.20
##  [7]       0.11       0.85       0.04       0.56       0.04
##  [1] -390735.21       0.63       0.11       0.21       0.05       0.21
##  [7]       0.11       0.85       0.04       0.56       0.04
##  [1] -390711.63       0.62       0.10       0.21       0.06       0.21
##  [7]       0.11       0.85       0.04       0.56       0.04
##  [1] -390692.85       0.62       0.10       0.22       0.06       0.21
##  [7]       0.11       0.85       0.04       0.56       0.04
##  [1] -390673.80       0.61       0.10       0.22       0.07       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390651.64       0.61       0.10       0.22       0.07       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390625.77       0.60       0.11       0.22       0.07       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390596.83       0.59       0.11       0.22       0.08       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390565.71       0.59       0.11       0.22       0.08       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390533.05       0.58       0.11       0.22       0.09       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390499.48       0.58       0.11       0.22       0.09       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390465.59       0.57       0.11       0.22       0.09       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390431.78       0.56       0.12       0.23       0.10       0.20
##  [7]       0.11       0.85       0.04       0.58       0.05
##  [1] -390398.38       0.56       0.12       0.23       0.10       0.20
##  [7]       0.11       0.85       0.04       0.58       0.05
##  [1] -390365.66       0.55       0.12       0.23       0.10       0.20
##  [7]       0.11       0.85       0.04       0.58       0.05
##  [1] -390333.75       0.55       0.12       0.23       0.11       0.20
##  [7]       0.10       0.85       0.04       0.58       0.05
##  [1] -390302.78       0.54       0.12       0.23       0.11       0.20
##  [7]       0.10       0.85       0.04       0.58       0.05
##  [1] -390272.89       0.53       0.13       0.23       0.11       0.20
##  [7]       0.10       0.85       0.04       0.58       0.05
##  [1] -390244.14       0.53       0.13       0.23       0.12       0.20
##  [7]       0.10       0.85       0.04       0.58       0.05
##  [1] -390216.59       0.52       0.13       0.23       0.12       0.20
##  [7]       0.10       0.85       0.04       0.58       0.05
##  [1] -390190.28       0.51       0.13       0.23       0.12       0.20
##  [7]       0.10       0.85       0.04       0.58       0.05
##  [1] -390165.23       0.51       0.13       0.23       0.13       0.20
##  [7]       0.10       0.85       0.04       0.58       0.05
##  [1] -390141.49       0.50       0.14       0.23       0.13       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -390118.97       0.50       0.14       0.23       0.13       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -390097.75       0.49       0.14       0.23       0.14       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -390077.78       0.48       0.14       0.23       0.14       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -390059.02       0.48       0.14       0.23       0.14       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -390041.47       0.47       0.15       0.23       0.15       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -390025.10       0.46       0.15       0.24       0.15       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -390009.88       0.46       0.15       0.24       0.16       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -389995.77       0.45       0.15       0.24       0.16       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -389982.74       0.45       0.15       0.24       0.16       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -389970.76       0.44       0.16       0.24       0.17       0.20
##  [7]       0.10       0.85       0.04       0.58       0.07
##  [1] -389959.79       0.43       0.16       0.24       0.17       0.20
##  [7]       0.10       0.85       0.04       0.58       0.07
##  [1] -389949.80       0.43       0.16       0.24       0.17       0.20
##  [7]       0.10       0.85       0.04       0.58       0.07
## [1] 19
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -399597.90       0.57       0.21       0.21       0.02       0.16
##  [7]       0.08       0.87       0.03       0.51       0.05
##  [1] -392507.68       0.61       0.18       0.19       0.03       0.17
##  [7]       0.08       0.86       0.03       0.52       0.05
##  [1] -391710.23       0.62       0.16       0.18       0.03       0.18
##  [7]       0.08       0.86       0.03       0.53       0.04
##  [1] -391450.54       0.63       0.15       0.18       0.04       0.18
##  [7]       0.08       0.85       0.03       0.54       0.04
##  [1] -391342.43       0.63       0.15       0.18       0.04       0.18
##  [7]       0.09       0.85       0.03       0.54       0.04
##  [1] -391295.44       0.63       0.14       0.18       0.05       0.19
##  [7]       0.09       0.85       0.03       0.55       0.04
##  [1] -391276.18       0.63       0.14       0.18       0.05       0.19
##  [7]       0.09       0.85       0.04       0.55       0.04
##  [1] -391269.00       0.62       0.14       0.18       0.06       0.18
##  [7]       0.08       0.85       0.04       0.56       0.04
## [1] 20
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -400914.74       0.58       0.20       0.20       0.02       0.16
##  [7]       0.08       0.87       0.03       0.51       0.05
##  [1] -392712.31       0.62       0.18       0.18       0.03       0.18
##  [7]       0.08       0.86       0.03       0.52       0.04
##  [1] -391819.32       0.63       0.16       0.17       0.03       0.19
##  [7]       0.08       0.85       0.03       0.53       0.04
##  [1] -391531.20       0.64       0.15       0.17       0.04       0.19
##  [7]       0.08       0.85       0.03       0.54       0.04
##  [1] -391407.01       0.64       0.15       0.17       0.05       0.20
##  [7]       0.08       0.85       0.03       0.54       0.04
##  [1] -391347.36       0.64       0.14       0.17       0.05       0.20
##  [7]       0.08       0.85       0.03       0.55       0.04
##  [1] -391316.93       0.63       0.14       0.17       0.06       0.20
##  [7]       0.08       0.84       0.03       0.55       0.04
##  [1] -391299.60       0.63       0.14       0.17       0.06       0.20
##  [7]       0.08       0.84       0.03       0.56       0.04
##  [1] -391287.10       0.62       0.14       0.17       0.07       0.20
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391275.59       0.61       0.14       0.17       0.07       0.20
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391262.07       0.61       0.15       0.17       0.08       0.20
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391245.40       0.60       0.15       0.17       0.08       0.20
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391225.64       0.59       0.15       0.18       0.09       0.20
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391203.00       0.58       0.15       0.18       0.09       0.20
##  [7]       0.08       0.84       0.04       0.57       0.04
##  [1] -391177.94       0.57       0.15       0.18       0.09       0.20
##  [7]       0.08       0.84       0.04       0.57       0.04
##  [1] -391152.52       0.57       0.16       0.18       0.10       0.20
##  [7]       0.08       0.84       0.04       0.57       0.04
##  [1] -391123.76       0.56       0.16       0.18       0.10       0.20
##  [7]       0.08       0.84       0.04       0.57       0.04
##  [1] -391094.77       0.55       0.16       0.18       0.11       0.20
##  [7]       0.08       0.84       0.04       0.57       0.05
##  [1] -391065.76       0.54       0.17       0.18       0.11       0.20
##  [7]       0.08       0.84       0.04       0.57       0.05
##  [1] -391037.17       0.53       0.17       0.19       0.11       0.20
##  [7]       0.08       0.84       0.04       0.57       0.05
##  [1] -391009.32       0.52       0.17       0.19       0.12       0.20
##  [7]       0.08       0.84       0.04       0.57       0.05
##  [1] -390982.50       0.52       0.17       0.19       0.12       0.20
##  [7]       0.08       0.84       0.04       0.57       0.05
##  [1] -390956.89       0.51       0.18       0.19       0.13       0.20
##  [7]       0.08       0.84       0.04       0.57       0.05
##  [1] -390932.64       0.50       0.18       0.19       0.13       0.20
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390909.87       0.49       0.18       0.19       0.14       0.20
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390888.60       0.48       0.19       0.19       0.14       0.20
##  [7]       0.08       0.85       0.03       0.57       0.05
##  [1] -390868.86       0.47       0.19       0.19       0.14       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390850.63       0.47       0.19       0.19       0.15       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390833.89       0.46       0.19       0.20       0.15       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390818.59       0.45       0.20       0.20       0.16       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390804.67       0.44       0.20       0.20       0.16       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390792.09       0.43       0.20       0.20       0.17       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390780.76       0.42       0.20       0.20       0.17       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390770.64       0.42       0.21       0.20       0.18       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390761.67       0.41       0.21       0.20       0.18       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
## [1] 21
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403647.99       0.60       0.24       0.14       0.02       0.16
##  [7]       0.08       0.86       0.03       0.51       0.05
##  [1] -393801.07       0.64       0.22       0.12       0.03       0.17
##  [7]       0.08       0.84       0.03       0.52       0.04
##  [1] -392537.71       0.65       0.21       0.11       0.04       0.18
##  [7]       0.08       0.83       0.03       0.53       0.04
##  [1] -392095.16       0.65       0.20       0.10       0.04       0.18
##  [7]       0.08       0.82       0.03       0.53       0.04
##  [1] -391922.77       0.65       0.19       0.10       0.05       0.18
##  [7]       0.08       0.81       0.03       0.54       0.04
##  [1] -391869.92       0.65       0.19       0.10       0.06       0.18
##  [7]       0.08       0.81       0.04       0.54       0.04
##  [1] -391870.44       0.64       0.19       0.11       0.07       0.18
##  [7]       0.08       0.80       0.04       0.54       0.04
## [1] 22
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -402847.53       0.59       0.24       0.15       0.02       0.16
##  [7]       0.08       0.86       0.03       0.51       0.05
##  [1] -393886.15       0.63       0.22       0.12       0.03       0.17
##  [7]       0.07       0.85       0.03       0.52       0.04
##  [1] -392760.66       0.64       0.21       0.11       0.03       0.17
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392377.06       0.65       0.20       0.11       0.04       0.18
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392231.32       0.65       0.20       0.11       0.05       0.18
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -392186.68       0.64       0.19       0.11       0.05       0.18
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -392185.73       0.64       0.19       0.11       0.06       0.18
##  [7]       0.07       0.81       0.04       0.54       0.04
## [1] 23
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -402801.75       0.59       0.23       0.16       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393639.57       0.63       0.21       0.14       0.03       0.17
##  [7]       0.07       0.85       0.03       0.52       0.05
##  [1] -392551.37       0.64       0.20       0.13       0.03       0.18
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392180.72       0.65       0.19       0.12       0.04       0.18
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392033.78       0.65       0.19       0.12       0.05       0.18
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391983.12       0.64       0.19       0.12       0.05       0.18
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391975.93       0.64       0.18       0.12       0.06       0.18
##  [7]       0.07       0.82       0.04       0.54       0.04
## [1] 24
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -404177.72       0.60       0.23       0.15       0.02       0.17
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -394036.85       0.64       0.21       0.12       0.03       0.18
##  [7]       0.07       0.85       0.04       0.52       0.04
##  [1] -392802.68       0.65       0.20       0.11       0.04       0.19
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392371.97       0.66       0.20       0.10       0.04       0.20
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392191.99       0.65       0.19       0.10       0.05       0.20
##  [7]       0.07       0.82       0.04       0.53       0.04
##  [1] -392121.30       0.65       0.19       0.10       0.06       0.20
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -392101.50       0.64       0.19       0.10       0.06       0.20
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -392102.06       0.63       0.19       0.10       0.07       0.20
##  [7]       0.07       0.81       0.05       0.54       0.04
## [1] 25
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -404482.56       0.61       0.23       0.14       0.02       0.17
##  [7]       0.07       0.86       0.03       0.51       0.05
##  [1] -393990.92       0.64       0.21       0.12       0.03       0.18
##  [7]       0.07       0.85       0.03       0.52       0.04
##  [1] -392686.41       0.66       0.20       0.11       0.04       0.19
##  [7]       0.07       0.83       0.03       0.52       0.04
##  [1] -392220.64       0.66       0.19       0.10       0.05       0.19
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392024.59       0.66       0.19       0.10       0.05       0.20
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -391949.61       0.65       0.19       0.10       0.06       0.20
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -391931.37       0.64       0.19       0.10       0.07       0.20
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -391935.15       0.63       0.19       0.10       0.08       0.20
##  [7]       0.07       0.80       0.04       0.54       0.04
## [1] 26
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -402869.78       0.59       0.26       0.14       0.02       0.15
##  [7]       0.07       0.86       0.03       0.51       0.05
##  [1] -393897.60       0.62       0.24       0.11       0.03       0.17
##  [7]       0.07       0.85       0.03       0.52       0.05
##  [1] -392820.30       0.64       0.23       0.10       0.03       0.17
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392440.62       0.64       0.22       0.10       0.04       0.17
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392283.37       0.64       0.22       0.09       0.05       0.17
##  [7]       0.07       0.82       0.04       0.53       0.04
##  [1] -392225.56       0.64       0.22       0.09       0.05       0.17
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -392214.34       0.63       0.22       0.09       0.06       0.17
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -392221.30       0.63       0.22       0.10       0.06       0.17
##  [7]       0.07       0.81       0.04       0.54       0.04
## [1] 27
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403547.91       0.59       0.25       0.14       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393838.80       0.63       0.23       0.11       0.03       0.18
##  [7]       0.07       0.85       0.03       0.51       0.04
##  [1] -392779.46       0.64       0.22       0.10       0.03       0.18
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392404.66       0.65       0.22       0.10       0.04       0.18
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392235.20       0.65       0.21       0.09       0.05       0.18
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392157.19       0.64       0.21       0.09       0.05       0.18
##  [7]       0.07       0.82       0.04       0.53       0.04
##  [1] -392124.18       0.64       0.21       0.09       0.06       0.18
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -392111.11       0.63       0.21       0.09       0.07       0.18
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -392103.47       0.62       0.21       0.10       0.07       0.18
##  [7]       0.07       0.81       0.05       0.54       0.04
## [1] 28
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403985.93       0.60       0.25       0.14       0.02       0.16
##  [7]       0.07       0.86       0.03       0.51       0.05
##  [1] -393904.32       0.63       0.23       0.11       0.03       0.18
##  [7]       0.07       0.85       0.03       0.52       0.04
##  [1] -392759.65       0.64       0.22       0.10       0.03       0.18
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392357.65       0.65       0.22       0.09       0.04       0.19
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392183.66       0.65       0.21       0.09       0.05       0.19
##  [7]       0.07       0.82       0.04       0.53       0.04
##  [1] -392111.90       0.64       0.21       0.09       0.06       0.19
##  [7]       0.07       0.82       0.04       0.53       0.04
##  [1] -392090.00       0.64       0.21       0.09       0.06       0.19
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -392089.45       0.63       0.21       0.09       0.07       0.19
##  [7]       0.07       0.81       0.04       0.54       0.04
## [1] 29
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -402127.58       0.58       0.25       0.15       0.02       0.15
##  [7]       0.08       0.87       0.03       0.51       0.05
##  [1] -393953.50       0.62       0.24       0.12       0.03       0.17
##  [7]       0.07       0.85       0.04       0.52       0.05
##  [1] -392980.52       0.64       0.22       0.11       0.03       0.17
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392629.74       0.64       0.22       0.10       0.04       0.17
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392477.38       0.64       0.21       0.10       0.05       0.17
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392413.92       0.64       0.21       0.10       0.05       0.17
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -392392.53       0.64       0.21       0.10       0.06       0.17
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -392388.13       0.63       0.21       0.10       0.06       0.17
##  [7]       0.07       0.82       0.04       0.54       0.04
## [1] 30
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403506.10       0.60       0.24       0.14       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -394385.31       0.63       0.22       0.11       0.03       0.18
##  [7]       0.07       0.85       0.04       0.52       0.04
##  [1] -393241.12       0.65       0.21       0.10       0.04       0.18
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392817.30       0.65       0.21       0.10       0.04       0.19
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392632.00       0.65       0.20       0.09       0.05       0.19
##  [7]       0.07       0.82       0.04       0.53       0.04
##  [1] -392557.26       0.65       0.20       0.09       0.06       0.19
##  [7]       0.07       0.82       0.05       0.54       0.04
##  [1] -392536.92       0.65       0.20       0.09       0.06       0.19
##  [7]       0.07       0.81       0.05       0.54       0.04
##  [1] -392540.01       0.64       0.20       0.09       0.07       0.19
##  [7]       0.07       0.81       0.05       0.54       0.04
## [1] 31
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403240.20       0.59       0.23       0.16       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393403.63       0.63       0.21       0.14       0.03       0.18
##  [7]       0.07       0.85       0.03       0.52       0.05
##  [1] -392255.93       0.64       0.19       0.13       0.03       0.18
##  [7]       0.07       0.84       0.03       0.53       0.04
##  [1] -391885.38       0.64       0.19       0.13       0.04       0.19
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -391746.01       0.64       0.18       0.13       0.05       0.19
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391699.79       0.64       0.18       0.13       0.05       0.19
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -391693.22       0.63       0.18       0.13       0.06       0.19
##  [7]       0.07       0.82       0.04       0.54       0.04
## [1] 32
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -402911.87       0.59       0.23       0.17       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393714.80       0.62       0.21       0.14       0.03       0.18
##  [7]       0.07       0.85       0.04       0.52       0.05
##  [1] -392592.72       0.64       0.19       0.13       0.03       0.18
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392230.87       0.65       0.19       0.13       0.04       0.19
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392097.95       0.65       0.18       0.13       0.04       0.19
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392055.26       0.64       0.18       0.13       0.05       0.19
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -392049.02       0.64       0.18       0.13       0.05       0.19
##  [7]       0.07       0.82       0.04       0.54       0.04
## [1] 33
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403904.05       0.59       0.20       0.18       0.02       0.18
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393101.84       0.63       0.19       0.16       0.03       0.20
##  [7]       0.06       0.86       0.04       0.51       0.05
##  [1] -391934.01       0.64       0.18       0.15       0.03       0.21
##  [7]       0.06       0.85       0.04       0.52       0.05
##  [1] -391592.67       0.64       0.18       0.14       0.04       0.22
##  [7]       0.06       0.85       0.04       0.52       0.05
##  [1] -391470.08       0.64       0.18       0.14       0.04       0.22
##  [7]       0.06       0.84       0.04       0.53       0.04
##  [1] -391426.83       0.63       0.18       0.14       0.05       0.22
##  [7]       0.06       0.84       0.04       0.53       0.04
##  [1] -391416.24       0.63       0.18       0.15       0.05       0.22
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -391418.69       0.62       0.18       0.15       0.06       0.22
##  [7]       0.06       0.83       0.05       0.54       0.04
## [1] 34
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -401732.65       0.57       0.26       0.15       0.02       0.15
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393375.68       0.61       0.24       0.12       0.03       0.16
##  [7]       0.07       0.85       0.03       0.51       0.04
##  [1] -392550.12       0.63       0.23       0.11       0.03       0.17
##  [7]       0.07       0.85       0.04       0.52       0.04
##  [1] -392288.08       0.63       0.22       0.11       0.04       0.17
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392178.39       0.63       0.22       0.10       0.04       0.17
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392127.30       0.63       0.22       0.10       0.05       0.17
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392100.32       0.63       0.22       0.10       0.05       0.17
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392081.06       0.62       0.21       0.10       0.06       0.16
##  [7]       0.06       0.83       0.04       0.53       0.04
##  [1] -392061.05       0.62       0.21       0.10       0.06       0.16
##  [7]       0.06       0.82       0.04       0.53       0.04
##  [1] -392035.34       0.61       0.22       0.10       0.07       0.16
##  [7]       0.06       0.82       0.04       0.54       0.04
##  [1] -392002.17       0.60       0.22       0.11       0.07       0.16
##  [7]       0.06       0.82       0.04       0.54       0.04
##  [1] -391961.38       0.60       0.22       0.11       0.08       0.16
##  [7]       0.06       0.82       0.04       0.53       0.04
##  [1] -391913.76       0.59       0.22       0.11       0.08       0.16
##  [7]       0.06       0.82       0.04       0.53       0.04
##  [1] -391860.69       0.58       0.22       0.11       0.09       0.16
##  [7]       0.06       0.82       0.04       0.53       0.05
##  [1] -391803.96       0.58       0.22       0.11       0.09       0.16
##  [7]       0.06       0.82       0.04       0.53       0.05
##  [1] -391744.88       0.57       0.22       0.11       0.09       0.16
##  [7]       0.06       0.82       0.04       0.53       0.05
##  [1] -391685.00       0.56       0.22       0.12       0.10       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391625.54       0.55       0.22       0.12       0.10       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391567.42       0.55       0.23       0.12       0.11       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391511.57       0.54       0.23       0.12       0.11       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391458.00       0.53       0.23       0.12       0.12       0.16
##  [7]       0.06       0.82       0.05       0.53       0.06
##  [1] -391407.30       0.52       0.23       0.12       0.12       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391359.62       0.52       0.23       0.13       0.12       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391314.99       0.51       0.23       0.13       0.13       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391273.38       0.50       0.24       0.13       0.13       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391234.68       0.49       0.24       0.13       0.14       0.15
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391198.76       0.49       0.24       0.13       0.14       0.15
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391165.49       0.48       0.24       0.14       0.15       0.15
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391134.70       0.47       0.24       0.14       0.15       0.15
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -391106.23       0.46       0.24       0.14       0.16       0.15
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -391079.92       0.45       0.24       0.14       0.16       0.15
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -391055.63       0.45       0.25       0.14       0.17       0.15
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -391033.23       0.44       0.25       0.15       0.17       0.15
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -391012.57       0.43       0.25       0.15       0.18       0.15
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -390993.55       0.42       0.25       0.15       0.18       0.15
##  [7]       0.05       0.82       0.05       0.51       0.07
##  [1] -390976.05       0.41       0.25       0.15       0.18       0.15
##  [7]       0.05       0.82       0.05       0.51       0.07
##  [1] -390959.97       0.41       0.25       0.15       0.19       0.15
##  [7]       0.05       0.82       0.05       0.51       0.08
##  [1] -390945.22       0.40       0.25       0.15       0.19       0.15
##  [7]       0.05       0.82       0.05       0.51       0.08
##  [1] -390931.72       0.39       0.25       0.16       0.20       0.15
##  [7]       0.05       0.82       0.05       0.51       0.08
##  [1] -390919.39       0.38       0.25       0.16       0.20       0.15
##  [7]       0.05       0.82       0.05       0.50       0.08
##  [1] -390908.16       0.38       0.26       0.16       0.21       0.15
##  [7]       0.05       0.82       0.05       0.50       0.08
##  [1] -390897.97       0.37       0.26       0.16       0.21       0.15
##  [7]       0.05       0.82       0.05       0.50       0.08
##  [1] -390888.75       0.36       0.26       0.16       0.22       0.15
##  [7]       0.05       0.82       0.05       0.50       0.08
## [1] 35
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -401850.66       0.57       0.25       0.16       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393221.70       0.61       0.23       0.13       0.03       0.17
##  [7]       0.07       0.86       0.03       0.52       0.05
##  [1] -392372.99       0.62       0.22       0.12       0.03       0.17
##  [7]       0.07       0.85       0.04       0.52       0.04
##  [1] -392119.38       0.63       0.22       0.12       0.04       0.17
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392022.92       0.63       0.21       0.12       0.04       0.17
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -391985.13       0.63       0.21       0.11       0.05       0.17
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -391970.90       0.63       0.21       0.11       0.05       0.17
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -391964.31       0.62       0.21       0.12       0.06       0.17
##  [7]       0.06       0.83       0.04       0.54       0.04
## [1] 36
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -401823.48       0.57       0.25       0.15       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393352.60       0.61       0.24       0.12       0.03       0.17
##  [7]       0.07       0.86       0.04       0.51       0.04
##  [1] -392519.40       0.62       0.23       0.11       0.03       0.17
##  [7]       0.07       0.85       0.04       0.52       0.04
##  [1] -392268.86       0.63       0.23       0.11       0.04       0.17
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392172.95       0.63       0.22       0.10       0.04       0.17
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392134.47       0.63       0.22       0.10       0.05       0.17
##  [7]       0.06       0.83       0.04       0.53       0.04
##  [1] -392118.38       0.63       0.22       0.10       0.05       0.17
##  [7]       0.06       0.83       0.04       0.53       0.04
##  [1] -392108.20       0.62       0.22       0.10       0.06       0.17
##  [7]       0.06       0.83       0.04       0.53       0.04
##  [1] -392095.12       0.62       0.22       0.10       0.06       0.17
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -392074.93       0.61       0.22       0.11       0.07       0.16
##  [7]       0.06       0.82       0.04       0.54       0.04
##  [1] -392046.15       0.60       0.22       0.11       0.07       0.16
##  [7]       0.06       0.82       0.04       0.54       0.04
##  [1] -392008.87       0.60       0.22       0.11       0.08       0.16
##  [7]       0.06       0.82       0.04       0.54       0.04
##  [1] -391964.11       0.59       0.22       0.11       0.08       0.16
##  [7]       0.06       0.82       0.04       0.53       0.04
##  [1] -391913.38       0.58       0.22       0.11       0.09       0.16
##  [7]       0.06       0.82       0.04       0.53       0.04
##  [1] -391858.64       0.58       0.22       0.11       0.09       0.16
##  [7]       0.06       0.82       0.04       0.53       0.04
##  [1] -391801.12       0.57       0.22       0.11       0.09       0.16
##  [7]       0.06       0.82       0.04       0.53       0.05
##  [1] -391742.47       0.56       0.22       0.12       0.10       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391683.95       0.55       0.23       0.12       0.10       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391626.52       0.55       0.23       0.12       0.11       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391571.13       0.54       0.23       0.12       0.11       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391517.83       0.53       0.23       0.12       0.11       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391467.22       0.52       0.23       0.13       0.12       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391419.47       0.52       0.23       0.13       0.12       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391374.65       0.51       0.24       0.13       0.13       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391332.73       0.50       0.24       0.13       0.13       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391293.63       0.49       0.24       0.13       0.13       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391257.24       0.49       0.24       0.13       0.14       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391223.42       0.48       0.24       0.14       0.14       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391192.01       0.47       0.24       0.14       0.15       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391162.88       0.46       0.25       0.14       0.15       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391135.87       0.46       0.25       0.14       0.16       0.16
##  [7]       0.06       0.82       0.05       0.52       0.07
##  [1] -391110.84       0.45       0.25       0.14       0.16       0.16
##  [7]       0.06       0.82       0.05       0.52       0.07
##  [1] -391087.66       0.44       0.25       0.15       0.16       0.16
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -391066.18       0.43       0.25       0.15       0.17       0.16
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -391046.31       0.43       0.25       0.15       0.17       0.15
##  [7]       0.05       0.82       0.05       0.51       0.07
##  [1] -391027.93       0.42       0.25       0.15       0.18       0.15
##  [7]       0.05       0.82       0.05       0.51       0.07
##  [1] -391010.93       0.41       0.25       0.15       0.18       0.15
##  [7]       0.05       0.82       0.05       0.51       0.07
##  [1] -390995.24       0.40       0.26       0.15       0.19       0.15
##  [7]       0.05       0.82       0.05       0.51       0.07
##  [1] -390980.76       0.40       0.26       0.16       0.19       0.15
##  [7]       0.05       0.82       0.05       0.51       0.07
##  [1] -390967.43       0.39       0.26       0.16       0.20       0.15
##  [7]       0.05       0.82       0.05       0.51       0.08
##  [1] -390955.16       0.38       0.26       0.16       0.20       0.15
##  [7]       0.05       0.82       0.05       0.51       0.08
##  [1] -390943.90       0.37       0.26       0.16       0.21       0.15
##  [7]       0.05       0.82       0.05       0.51       0.08
##  [1] -390933.58       0.37       0.26       0.16       0.21       0.15
##  [7]       0.05       0.83       0.05       0.51       0.08
##  [1] -390924.16       0.36       0.26       0.16       0.21       0.15
##  [7]       0.05       0.83       0.05       0.51       0.08
## [1] 37
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -401646.97       0.58       0.23       0.17       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -392856.08       0.61       0.21       0.15       0.03       0.17
##  [7]       0.07       0.86       0.03       0.52       0.05
##  [1] -391939.60       0.63       0.20       0.14       0.03       0.17
##  [7]       0.07       0.85       0.03       0.53       0.04
##  [1] -391634.20       0.63       0.19       0.14       0.04       0.17
##  [7]       0.07       0.84       0.03       0.53       0.04
##  [1] -391506.99       0.63       0.18       0.14       0.04       0.17
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -391455.22       0.63       0.18       0.14       0.05       0.17
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -391438.02       0.63       0.18       0.14       0.05       0.17
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391434.36       0.62       0.18       0.14       0.06       0.17
##  [7]       0.07       0.83       0.04       0.55       0.04
## [1] 38
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -402091.04       0.58       0.23       0.17       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -392947.65       0.62       0.21       0.14       0.03       0.17
##  [7]       0.07       0.85       0.03       0.52       0.05
##  [1] -391982.95       0.63       0.20       0.14       0.03       0.17
##  [7]       0.07       0.84       0.03       0.53       0.04
##  [1] -391665.86       0.64       0.19       0.13       0.04       0.17
##  [7]       0.07       0.84       0.03       0.53       0.04
##  [1] -391536.11       0.64       0.19       0.13       0.04       0.17
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391485.04       0.63       0.18       0.13       0.05       0.17
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391469.83       0.63       0.18       0.13       0.06       0.17
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391468.32       0.62       0.18       0.14       0.06       0.17
##  [7]       0.07       0.83       0.04       0.55       0.04
## [1] 39
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -400190.16       0.56       0.24       0.18       0.02       0.15
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -392404.48       0.59       0.22       0.16       0.02       0.16
##  [7]       0.07       0.86       0.03       0.52       0.05
##  [1] -391577.56       0.61       0.21       0.16       0.03       0.16
##  [7]       0.07       0.85       0.03       0.53       0.05
##  [1] -391319.07       0.62       0.20       0.15       0.03       0.16
##  [7]       0.07       0.85       0.03       0.54       0.04
##  [1] -391227.25       0.62       0.19       0.15       0.04       0.16
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -391205.47       0.62       0.19       0.15       0.04       0.16
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -391214.81       0.61       0.19       0.15       0.05       0.15
##  [7]       0.06       0.84       0.04       0.55       0.04
## [1] 40
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -400741.31       0.57       0.25       0.16       0.02       0.15
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393228.22       0.61       0.23       0.13       0.03       0.16
##  [7]       0.07       0.86       0.03       0.52       0.04
##  [1] -392527.82       0.62       0.22       0.12       0.03       0.17
##  [7]       0.07       0.85       0.04       0.52       0.04
##  [1] -392307.96       0.63       0.22       0.12       0.04       0.17
##  [7]       0.07       0.85       0.04       0.53       0.04
##  [1] -392212.22       0.63       0.21       0.11       0.04       0.17
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392164.22       0.63       0.21       0.11       0.05       0.16
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392136.77       0.63       0.21       0.11       0.05       0.16
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -392117.62       0.63       0.20       0.11       0.06       0.16
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -392098.58       0.62       0.20       0.11       0.06       0.16
##  [7]       0.06       0.84       0.04       0.54       0.04
##  [1] -392075.68       0.62       0.20       0.11       0.07       0.16
##  [7]       0.06       0.84       0.04       0.54       0.04
##  [1] -392047.06       0.61       0.20       0.11       0.07       0.16
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -392012.25       0.60       0.20       0.11       0.08       0.16
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -391971.56       0.60       0.21       0.12       0.08       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391925.96       0.59       0.21       0.12       0.08       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391876.63       0.59       0.21       0.12       0.09       0.15
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391825.04       0.58       0.21       0.12       0.09       0.15
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391772.23       0.57       0.21       0.12       0.10       0.15
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391719.71       0.57       0.21       0.12       0.10       0.15
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391668.19       0.56       0.21       0.12       0.10       0.15
##  [7]       0.06       0.84       0.04       0.54       0.05
##  [1] -391618.50       0.55       0.21       0.13       0.11       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391571.22       0.55       0.21       0.13       0.11       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391526.75       0.54       0.22       0.13       0.12       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391485.32       0.53       0.22       0.13       0.12       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391447.05       0.52       0.22       0.13       0.13       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391411.95       0.52       0.22       0.13       0.13       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391379.97       0.51       0.22       0.13       0.14       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391351.01       0.50       0.22       0.13       0.14       0.15
##  [7]       0.06       0.84       0.04       0.53       0.07
##  [1] -391324.93       0.50       0.22       0.14       0.14       0.15
##  [7]       0.06       0.84       0.04       0.53       0.07
##  [1] -391301.57       0.49       0.22       0.14       0.15       0.15
##  [7]       0.06       0.84       0.04       0.52       0.07
##  [1] -391280.77       0.48       0.23       0.14       0.15       0.15
##  [7]       0.06       0.84       0.04       0.52       0.07
##  [1] -391262.36       0.47       0.23       0.14       0.16       0.15
##  [7]       0.06       0.84       0.04       0.52       0.07
##  [1] -391246.18       0.47       0.23       0.14       0.16       0.15
##  [7]       0.06       0.84       0.04       0.52       0.07
##  [1] -391232.08       0.46       0.23       0.14       0.17       0.15
##  [7]       0.05       0.84       0.04       0.52       0.07
##  [1] -391219.90       0.45       0.23       0.14       0.17       0.15
##  [7]       0.05       0.84       0.04       0.52       0.08
##  [1] -391209.51       0.45       0.23       0.14       0.18       0.15
##  [7]       0.05       0.84       0.04       0.52       0.08
##  [1] -391200.83       0.44       0.23       0.15       0.18       0.15
##  [7]       0.05       0.84       0.04       0.52       0.08
## [1] 41
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -401299.92       0.58       0.24       0.16       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393019.54       0.61       0.23       0.13       0.03       0.17
##  [7]       0.07       0.86       0.03       0.52       0.04
##  [1] -392273.34       0.63       0.21       0.12       0.03       0.17
##  [7]       0.07       0.85       0.03       0.52       0.04
##  [1] -392032.83       0.64       0.21       0.12       0.04       0.17
##  [7]       0.07       0.85       0.03       0.53       0.04
##  [1] -391924.78       0.64       0.20       0.12       0.05       0.17
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -391870.43       0.64       0.20       0.11       0.05       0.17
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -391840.92       0.63       0.20       0.11       0.06       0.17
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -391822.46       0.63       0.20       0.11       0.06       0.16
##  [7]       0.06       0.84       0.04       0.54       0.04
##  [1] -391805.34       0.62       0.20       0.12       0.07       0.16
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -391784.51       0.61       0.20       0.12       0.07       0.16
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -391757.56       0.61       0.20       0.12       0.08       0.16
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -391723.87       0.60       0.20       0.12       0.08       0.16
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -391683.69       0.59       0.20       0.12       0.09       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391638.31       0.58       0.20       0.12       0.09       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391588.76       0.57       0.20       0.12       0.10       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391537.02       0.57       0.20       0.13       0.10       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391484.59       0.56       0.20       0.13       0.11       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391432.83       0.55       0.21       0.13       0.11       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391382.86       0.54       0.21       0.13       0.12       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391335.37       0.53       0.21       0.13       0.12       0.16
##  [7]       0.06       0.83       0.04       0.54       0.06
##  [1] -391290.96       0.53       0.21       0.13       0.13       0.15
##  [7]       0.06       0.83       0.04       0.54       0.06
##  [1] -391250.01       0.52       0.21       0.14       0.13       0.15
##  [7]       0.06       0.83       0.04       0.54       0.06
##  [1] -391212.68       0.51       0.21       0.14       0.14       0.15
##  [7]       0.06       0.83       0.04       0.54       0.06
##  [1] -391179.03       0.50       0.22       0.14       0.14       0.15
##  [7]       0.06       0.83       0.04       0.53       0.06
##  [1] -391148.98       0.49       0.22       0.14       0.15       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391122.42       0.48       0.22       0.14       0.16       0.15
##  [7]       0.06       0.84       0.04       0.53       0.07
##  [1] -391099.15       0.47       0.22       0.14       0.16       0.15
##  [7]       0.06       0.84       0.04       0.53       0.07
##  [1] -391078.99       0.47       0.22       0.14       0.17       0.15
##  [7]       0.05       0.84       0.04       0.53       0.07
##  [1] -391061.73       0.46       0.22       0.15       0.17       0.15
##  [7]       0.05       0.84       0.04       0.53       0.07
##  [1] -391047.15       0.45       0.23       0.15       0.18       0.15
##  [7]       0.05       0.84       0.04       0.53       0.07
##  [1] -391035.12       0.44       0.23       0.15       0.18       0.15
##  [7]       0.05       0.84       0.04       0.53       0.07
##  [1] -391025.34       0.43       0.23       0.15       0.19       0.15
##  [7]       0.05       0.84       0.04       0.53       0.07
## [1] 42
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -400462.75       0.57       0.25       0.16       0.02       0.15
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393099.99       0.61       0.23       0.14       0.03       0.16
##  [7]       0.07       0.86       0.03       0.52       0.04
##  [1] -392431.12       0.62       0.22       0.12       0.03       0.16
##  [7]       0.07       0.85       0.03       0.52       0.04
##  [1] -392211.50       0.63       0.21       0.12       0.04       0.16
##  [7]       0.07       0.85       0.04       0.53       0.04
##  [1] -392110.42       0.63       0.21       0.12       0.04       0.16
##  [7]       0.07       0.85       0.04       0.53       0.04
##  [1] -392057.18       0.63       0.21       0.11       0.05       0.16
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392025.77       0.63       0.20       0.11       0.05       0.16
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -392003.93       0.63       0.20       0.11       0.06       0.16
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -391983.17       0.62       0.20       0.11       0.06       0.16
##  [7]       0.06       0.84       0.04       0.54       0.04
##  [1] -391959.17       0.62       0.20       0.12       0.07       0.16
##  [7]       0.06       0.84       0.04       0.54       0.04
##  [1] -391929.79       0.61       0.20       0.12       0.07       0.15
##  [7]       0.06       0.84       0.04       0.54       0.04
##  [1] -391894.34       0.60       0.20       0.12       0.08       0.15
##  [7]       0.06       0.84       0.04       0.54       0.04
##  [1] -391853.10       0.60       0.20       0.12       0.08       0.15
##  [7]       0.06       0.84       0.04       0.54       0.05
##  [1] -391807.07       0.59       0.20       0.12       0.09       0.15
##  [7]       0.06       0.84       0.04       0.54       0.05
##  [1] -391757.19       0.59       0.20       0.12       0.09       0.15
##  [7]       0.06       0.84       0.04       0.54       0.05
##  [1] -391705.00       0.58       0.21       0.12       0.09       0.15
##  [7]       0.06       0.84       0.04       0.54       0.05
##  [1] -391651.85       0.57       0.21       0.12       0.10       0.15
##  [7]       0.06       0.84       0.04       0.54       0.05
##  [1] -391599.12       0.57       0.21       0.12       0.10       0.15
##  [7]       0.06       0.84       0.04       0.54       0.05
##  [1] -391547.56       0.56       0.21       0.13       0.11       0.15
##  [7]       0.06       0.84       0.04       0.54       0.06
##  [1] -391498.05       0.55       0.21       0.13       0.11       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391451.20       0.55       0.21       0.13       0.12       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391407.43       0.54       0.21       0.13       0.12       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391366.98       0.53       0.21       0.13       0.12       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391329.96       0.52       0.21       0.13       0.13       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391296.39       0.52       0.22       0.13       0.13       0.15
##  [7]       0.06       0.84       0.04       0.53       0.07
##  [1] -391266.20       0.51       0.22       0.13       0.14       0.15
##  [7]       0.06       0.84       0.04       0.53       0.07
##  [1] -391239.26       0.50       0.22       0.14       0.14       0.15
##  [7]       0.06       0.84       0.04       0.53       0.07
##  [1] -391215.42       0.49       0.22       0.14       0.15       0.14
##  [7]       0.05       0.84       0.04       0.53       0.07
##  [1] -391194.51       0.49       0.22       0.14       0.15       0.14
##  [7]       0.05       0.84       0.04       0.52       0.07
##  [1] -391176.35       0.48       0.22       0.14       0.16       0.14
##  [7]       0.05       0.84       0.04       0.52       0.07
##  [1] -391160.74       0.47       0.22       0.14       0.16       0.14
##  [7]       0.05       0.84       0.04       0.52       0.07
##  [1] -391147.52       0.46       0.22       0.14       0.17       0.14
##  [7]       0.05       0.84       0.04       0.52       0.08
##  [1] -391136.51       0.46       0.23       0.14       0.17       0.14
##  [7]       0.05       0.84       0.04       0.52       0.08
##  [1] -391127.60       0.45       0.23       0.15       0.18       0.14
##  [7]       0.05       0.84       0.04       0.52       0.08
validation_epic.organoid$thresholded_ratio_max<-F
validation_epic.organoid$thresholded_ratio_max[which(validation_epic.organoid$thresholded_prior_ratio>1)]<-T

percent_passing<-round((tapply(validation_epic.organoid$thresholded_ratio_max, validation_epic.organoid$passage_hilo, sum)/tapply(validation_epic.organoid$array.id, validation_epic.organoid$passage_hilo, length))*100,2)
passed_num<-tapply(validation_epic.organoid$thresholded_ratio_max, validation_epic.organoid$passage_hilo, sum)
org_numer<-tapply(validation_epic.organoid$array.id, validation_epic.organoid$passage_hilo, length)

df<-data.frame(passage=names(percent_passing), passing=percent_passing, pro_passing=percent_passing/100, count=org_numer, passed_num=passed_num)
df<-cbind(df,(binom.confint(df$passed_num, df$count, method="exact", conf.level=0.95)))
df$upper<-df$upper*100
df$lower<-df$lower*100

print(df)
##      passage passing pro_passing count passed_num method x  n      mean
## high    high   38.10      0.3810    21          8  exact 8 21 0.3809524
## low      low   14.29      0.1429    21          3  exact 3 21 0.1428571
##          lower    upper
## high 18.107163 61.56456
## low   3.048897 36.34240

Plot all samples

plts_paired<-lapply(1:nrow(validation_epic.organoid), function(x){#1:nrow(validation_epic.organoid)
  print(x)
  passage<-paste("passage: ",validation_epic.organoid$passage[x],"\nIndividual: ", validation_epic.organoid$Sample_Name[x],"\nRatio I/H: ",round(validation_epic.organoid$thresholded_prior_ratio[x],2), sep="")
  converted<-as.numeric(round(validation_organoid_beta_VeryVariable[,x]*1000,0))
  counts<-rep(1000, length(converted))
  res = em(converted, counts, .41, .31, .27, 0.01, .1, .1, .90, .03, .5, .05)
  draw_fit_params_gg(converted, counts, res,passage)
})
## [1] 1
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -397515.94       0.55       0.25       0.18       0.02       0.15
##  [7]       0.07       0.88       0.03       0.51       0.05
##  [1] -391627.52       0.58       0.24       0.16       0.02       0.15
##  [7]       0.07       0.87       0.03       0.52       0.04
##  [1] -391311.14       0.60       0.22       0.15       0.03       0.15
##  [7]       0.07       0.87       0.03       0.52       0.04
##  [1] -391271.60       0.61       0.22       0.14       0.04       0.15
##  [7]       0.06       0.87       0.03       0.52       0.04
##  [1] -391279.02       0.61       0.21       0.13       0.04       0.15
##  [7]       0.06       0.86       0.03       0.53       0.04
## [1] 2
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -397366.29       0.54       0.25       0.18       0.02       0.15
##  [7]       0.07       0.88       0.03       0.51       0.05
##  [1] -391640.40       0.58       0.24       0.16       0.02       0.15
##  [7]       0.07       0.87       0.03       0.51       0.04
##  [1] -391333.52       0.60       0.23       0.15       0.03       0.15
##  [7]       0.07       0.87       0.03       0.52       0.04
##  [1] -391300.52       0.61       0.22       0.14       0.04       0.15
##  [7]       0.06       0.87       0.03       0.52       0.04
##  [1] -391314.51       0.61       0.21       0.14       0.04       0.15
##  [7]       0.06       0.87       0.03       0.53       0.04
##  [1] -391337.56       0.61       0.21       0.14       0.05       0.14
##  [7]       0.06       0.87       0.03       0.53       0.04
##  [1] -391359.52       0.61       0.20       0.13       0.05       0.14
##  [7]       0.06       0.87       0.03       0.53       0.04
##  [1] -391372.26       0.61       0.20       0.13       0.06       0.14
##  [7]       0.05       0.87       0.03       0.53       0.04
##  [1] -391373.64       0.61       0.20       0.13       0.06       0.14
##  [7]       0.05       0.87       0.03       0.53       0.04
## [1] 3
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -399244.49       0.56       0.23       0.19       0.02       0.15
##  [7]       0.08       0.88       0.03       0.51       0.05
##  [1] -392243.87       0.59       0.21       0.17       0.02       0.16
##  [7]       0.07       0.87       0.03       0.52       0.05
##  [1] -391647.41       0.61       0.20       0.16       0.03       0.17
##  [7]       0.07       0.86       0.03       0.53       0.04
##  [1] -391483.96       0.62       0.19       0.16       0.03       0.17
##  [7]       0.07       0.86       0.03       0.53       0.04
##  [1] -391420.21       0.62       0.18       0.16       0.04       0.17
##  [7]       0.07       0.86       0.03       0.54       0.04
##  [1] -391392.00       0.62       0.18       0.16       0.04       0.17
##  [7]       0.07       0.85       0.03       0.54       0.04
##  [1] -391379.20       0.62       0.17       0.16       0.05       0.17
##  [7]       0.07       0.85       0.03       0.54       0.04
##  [1] -391372.70       0.62       0.17       0.16       0.05       0.16
##  [7]       0.07       0.85       0.03       0.55       0.04
## [1] 4
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -398551.07       0.55       0.23       0.20       0.02       0.15
##  [7]       0.07       0.88       0.03       0.51       0.05
##  [1] -392065.62       0.59       0.21       0.18       0.02       0.16
##  [7]       0.07       0.87       0.03       0.52       0.04
##  [1] -391596.77       0.61       0.19       0.17       0.03       0.17
##  [7]       0.07       0.87       0.03       0.52       0.04
##  [1] -391474.81       0.62       0.19       0.16       0.04       0.17
##  [7]       0.07       0.86       0.03       0.53       0.04
##  [1] -391423.89       0.62       0.18       0.16       0.04       0.17
##  [7]       0.07       0.86       0.03       0.54       0.04
##  [1] -391395.66       0.62       0.18       0.16       0.04       0.17
##  [7]       0.07       0.86       0.03       0.54       0.04
##  [1] -391376.19       0.62       0.17       0.16       0.05       0.17
##  [7]       0.07       0.86       0.03       0.54       0.04
##  [1] -391359.68       0.62       0.17       0.16       0.05       0.16
##  [7]       0.07       0.86       0.03       0.55       0.04
##  [1] -391343.96       0.62       0.17       0.16       0.06       0.16
##  [7]       0.07       0.86       0.03       0.55       0.04
##  [1] -391325.61       0.61       0.17       0.16       0.06       0.16
##  [7]       0.06       0.86       0.03       0.55       0.04
##  [1] -391303.71       0.61       0.17       0.16       0.07       0.16
##  [7]       0.06       0.86       0.03       0.55       0.04
##  [1] -391277.80       0.60       0.17       0.16       0.07       0.16
##  [7]       0.06       0.86       0.03       0.55       0.05
##  [1] -391247.99       0.60       0.17       0.16       0.08       0.16
##  [7]       0.06       0.86       0.03       0.55       0.05
##  [1] -391214.76       0.59       0.17       0.16       0.08       0.16
##  [7]       0.06       0.86       0.03       0.56       0.05
##  [1] -391178.90       0.59       0.17       0.16       0.08       0.16
##  [7]       0.06       0.86       0.03       0.56       0.05
##  [1] -391141.28       0.58       0.17       0.16       0.09       0.15
##  [7]       0.06       0.87       0.03       0.56       0.05
##  [1] -391102.71       0.58       0.17       0.16       0.09       0.15
##  [7]       0.06       0.87       0.03       0.56       0.05
##  [1] -391064.15       0.57       0.17       0.16       0.10       0.15
##  [7]       0.06       0.87       0.03       0.56       0.05
##  [1] -391026.39       0.57       0.18       0.16       0.10       0.15
##  [7]       0.06       0.87       0.03       0.56       0.06
##  [1] -390990.11       0.56       0.18       0.16       0.10       0.15
##  [7]       0.06       0.87       0.03       0.56       0.06
##  [1] -390955.86       0.56       0.18       0.16       0.11       0.15
##  [7]       0.06       0.87       0.03       0.56       0.06
##  [1] -390924.08       0.55       0.18       0.16       0.11       0.15
##  [7]       0.06       0.87       0.03       0.56       0.06
##  [1] -390895.07       0.55       0.18       0.16       0.12       0.15
##  [7]       0.06       0.87       0.03       0.56       0.06
##  [1] -390869.01       0.54       0.18       0.16       0.12       0.15
##  [7]       0.06       0.87       0.03       0.56       0.07
##  [1] -390846.05       0.53       0.18       0.16       0.12       0.15
##  [7]       0.06       0.87       0.03       0.56       0.07
##  [1] -390826.23       0.53       0.18       0.16       0.13       0.15
##  [7]       0.06       0.87       0.03       0.56       0.07
##  [1] -390809.51       0.52       0.18       0.16       0.13       0.15
##  [7]       0.06       0.87       0.03       0.56       0.07
##  [1] -390795.83       0.52       0.18       0.16       0.14       0.15
##  [7]       0.05       0.87       0.03       0.56       0.07
##  [1] -390785.07       0.51       0.19       0.16       0.14       0.15
##  [7]       0.05       0.87       0.03       0.56       0.08
##  [1] -390777.10       0.50       0.19       0.16       0.15       0.15
##  [7]       0.05       0.87       0.03       0.56       0.08
## [1] 5
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -401736.10       0.57       0.26       0.15       0.02       0.15
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393400.10       0.61       0.24       0.12       0.03       0.16
##  [7]       0.07       0.85       0.03       0.52       0.05
##  [1] -392470.87       0.62       0.23       0.11       0.03       0.16
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392163.86       0.63       0.23       0.11       0.04       0.16
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392045.42       0.63       0.22       0.10       0.04       0.16
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392005.88       0.63       0.22       0.10       0.05       0.16
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391999.88       0.63       0.22       0.10       0.05       0.16
##  [7]       0.06       0.82       0.04       0.54       0.04
## [1] 6
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403181.16       0.59       0.25       0.14       0.02       0.16
##  [7]       0.07       0.86       0.03       0.51       0.05
##  [1] -393624.52       0.62       0.24       0.11       0.03       0.17
##  [7]       0.07       0.85       0.03       0.52       0.04
##  [1] -392548.39       0.64       0.23       0.10       0.03       0.17
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392184.71       0.64       0.22       0.09       0.04       0.17
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392038.21       0.64       0.22       0.09       0.05       0.17
##  [7]       0.07       0.82       0.04       0.53       0.04
##  [1] -391983.60       0.64       0.22       0.09       0.05       0.17
##  [7]       0.06       0.82       0.04       0.53       0.04
##  [1] -391969.28       0.63       0.22       0.09       0.06       0.17
##  [7]       0.06       0.81       0.04       0.54       0.04
##  [1] -391968.67       0.62       0.22       0.09       0.07       0.17
##  [7]       0.06       0.81       0.04       0.54       0.04
## [1] 7
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -404190.72       0.60       0.24       0.14       0.02       0.16
##  [7]       0.07       0.86       0.03       0.51       0.05
##  [1] -393891.24       0.64       0.22       0.11       0.03       0.17
##  [7]       0.07       0.84       0.03       0.52       0.04
##  [1] -392563.39       0.65       0.21       0.11       0.04       0.18
##  [7]       0.07       0.83       0.03       0.53       0.04
##  [1] -392120.86       0.65       0.20       0.10       0.04       0.18
##  [7]       0.07       0.82       0.03       0.53       0.04
##  [1] -391966.08       0.65       0.20       0.10       0.05       0.18
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -391933.91       0.64       0.20       0.10       0.06       0.18
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -391953.46       0.64       0.20       0.10       0.06       0.18
##  [7]       0.07       0.80       0.04       0.54       0.04
##  [1] -391988.49       0.63       0.20       0.11       0.07       0.18
##  [7]       0.07       0.80       0.04       0.55       0.04
##  [1] -392018.66       0.62       0.20       0.11       0.08       0.18
##  [7]       0.07       0.80       0.04       0.55       0.04
##  [1] -392034.98       0.61       0.20       0.11       0.08       0.18
##  [7]       0.07       0.79       0.04       0.55       0.04
##  [1] -392034.36       0.59       0.21       0.11       0.09       0.18
##  [7]       0.07       0.79       0.04       0.55       0.04
## [1] 8
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -402715.66       0.58       0.24       0.15       0.02       0.16
##  [7]       0.07       0.86       0.03       0.51       0.05
##  [1] -393422.88       0.62       0.23       0.13       0.03       0.17
##  [7]       0.07       0.85       0.03       0.52       0.05
##  [1] -392383.64       0.63       0.22       0.12       0.03       0.17
##  [7]       0.07       0.84       0.03       0.53       0.04
##  [1] -392049.59       0.64       0.21       0.12       0.04       0.18
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -391925.07       0.64       0.20       0.12       0.04       0.18
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391886.99       0.63       0.20       0.12       0.05       0.18
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -391886.54       0.63       0.20       0.12       0.05       0.18
##  [7]       0.07       0.82       0.04       0.54       0.04
## [1] 9
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -401261.69       0.58       0.21       0.19       0.02       0.16
##  [7]       0.08       0.87       0.03       0.51       0.05
##  [1] -392806.79       0.62       0.18       0.17       0.03       0.18
##  [7]       0.08       0.86       0.03       0.52       0.04
##  [1] -391920.67       0.64       0.17       0.16       0.03       0.19
##  [7]       0.08       0.85       0.03       0.53       0.04
##  [1] -391632.83       0.65       0.16       0.16       0.04       0.19
##  [7]       0.08       0.85       0.03       0.54       0.04
##  [1] -391502.84       0.65       0.15       0.15       0.05       0.19
##  [7]       0.08       0.84       0.03       0.54       0.04
##  [1] -391434.58       0.64       0.15       0.15       0.06       0.19
##  [7]       0.08       0.84       0.03       0.55       0.04
##  [1] -391394.46       0.64       0.14       0.16       0.06       0.20
##  [7]       0.08       0.84       0.03       0.55       0.04
##  [1] -391367.24       0.63       0.14       0.16       0.07       0.20
##  [7]       0.08       0.84       0.03       0.55       0.04
##  [1] -391345.65       0.62       0.14       0.16       0.07       0.19
##  [7]       0.08       0.84       0.03       0.55       0.04
##  [1] -391324.99       0.62       0.15       0.16       0.08       0.19
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391303.07       0.61       0.15       0.16       0.08       0.19
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391279.08       0.60       0.15       0.16       0.09       0.19
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391252.94       0.59       0.15       0.16       0.09       0.19
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391224.95       0.58       0.15       0.17       0.10       0.19
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391195.57       0.57       0.16       0.17       0.10       0.19
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391165.37       0.56       0.16       0.17       0.11       0.19
##  [7]       0.08       0.84       0.04       0.56       0.05
##  [1] -391134.91       0.55       0.16       0.17       0.11       0.19
##  [7]       0.08       0.84       0.04       0.56       0.05
##  [1] -391105.88       0.54       0.16       0.17       0.12       0.19
##  [7]       0.08       0.84       0.04       0.56       0.05
##  [1] -391075.56       0.54       0.17       0.17       0.12       0.19
##  [7]       0.08       0.84       0.04       0.56       0.05
##  [1] -391046.95       0.53       0.17       0.18       0.13       0.19
##  [7]       0.08       0.84       0.04       0.56       0.05
##  [1] -391020.14       0.52       0.17       0.18       0.13       0.19
##  [7]       0.08       0.84       0.04       0.56       0.05
##  [1] -390995.03       0.51       0.18       0.18       0.14       0.19
##  [7]       0.08       0.84       0.04       0.56       0.05
##  [1] -390971.85       0.50       0.18       0.18       0.14       0.19
##  [7]       0.08       0.84       0.03       0.56       0.05
##  [1] -390950.61       0.49       0.18       0.18       0.15       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
##  [1] -390931.35       0.48       0.18       0.18       0.15       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
##  [1] -390914.09       0.47       0.19       0.18       0.16       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
##  [1] -390898.81       0.46       0.19       0.19       0.16       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
##  [1] -390885.44       0.45       0.19       0.19       0.17       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
##  [1] -390873.91       0.44       0.19       0.19       0.17       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
##  [1] -390863.90       0.44       0.20       0.19       0.18       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
##  [1] -390855.79       0.43       0.20       0.19       0.18       0.19
##  [7]       0.08       0.84       0.03       0.56       0.06
## [1] 10
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -400720.44       0.58       0.20       0.20       0.02       0.17
##  [7]       0.08       0.87       0.03       0.51       0.05
##  [1] -392763.80       0.62       0.17       0.18       0.03       0.19
##  [7]       0.08       0.87       0.03       0.52       0.04
##  [1] -391942.07       0.64       0.15       0.17       0.04       0.20
##  [7]       0.08       0.86       0.03       0.53       0.04
##  [1] -391656.08       0.65       0.15       0.16       0.04       0.20
##  [7]       0.08       0.86       0.03       0.53       0.04
##  [1] -391516.99       0.65       0.14       0.16       0.05       0.21
##  [7]       0.08       0.85       0.04       0.54       0.04
##  [1] -391436.11       0.65       0.14       0.16       0.06       0.21
##  [7]       0.08       0.85       0.04       0.55       0.04
##  [1] -391381.68       0.64       0.13       0.16       0.06       0.21
##  [7]       0.08       0.85       0.04       0.55       0.04
##  [1] -391339.68       0.63       0.13       0.16       0.07       0.21
##  [7]       0.08       0.85       0.04       0.55       0.04
##  [1] -391303.39       0.63       0.13       0.17       0.07       0.21
##  [7]       0.08       0.85       0.04       0.56       0.04
##  [1] -391270.19       0.62       0.14       0.17       0.08       0.21
##  [7]       0.08       0.85       0.04       0.56       0.04
##  [1] -391237.85       0.61       0.14       0.17       0.08       0.21
##  [7]       0.08       0.85       0.04       0.56       0.04
##  [1] -391205.97       0.60       0.14       0.17       0.09       0.21
##  [7]       0.08       0.85       0.04       0.56       0.04
##  [1] -391174.14       0.59       0.14       0.17       0.09       0.21
##  [7]       0.08       0.85       0.04       0.56       0.04
##  [1] -391143.01       0.59       0.14       0.17       0.10       0.21
##  [7]       0.08       0.85       0.04       0.56       0.04
##  [1] -391112.14       0.58       0.15       0.17       0.10       0.21
##  [7]       0.08       0.85       0.04       0.57       0.04
##  [1] -391082.01       0.57       0.15       0.18       0.11       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -391052.94       0.56       0.15       0.18       0.11       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -391025.10       0.55       0.16       0.18       0.12       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390998.66       0.54       0.16       0.18       0.12       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390973.70       0.53       0.16       0.18       0.13       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390950.37       0.52       0.16       0.18       0.13       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390928.73       0.51       0.17       0.18       0.14       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390908.84       0.51       0.17       0.18       0.14       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390890.72       0.50       0.17       0.19       0.15       0.21
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390874.38       0.49       0.18       0.19       0.15       0.21
##  [7]       0.08       0.85       0.04       0.57       0.06
##  [1] -390859.78       0.48       0.18       0.19       0.15       0.21
##  [7]       0.08       0.86       0.04       0.57       0.06
##  [1] -390846.90       0.47       0.18       0.19       0.16       0.21
##  [7]       0.08       0.86       0.04       0.57       0.06
##  [1] -390835.69       0.46       0.18       0.19       0.17       0.21
##  [7]       0.08       0.86       0.04       0.57       0.06
##  [1] -390826.09       0.45       0.19       0.19       0.17       0.21
##  [7]       0.08       0.86       0.03       0.57       0.06
## [1] 11
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -400291.39       0.57       0.23       0.19       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -392644.37       0.61       0.21       0.16       0.03       0.17
##  [7]       0.07       0.87       0.03       0.52       0.04
##  [1] -392023.33       0.62       0.19       0.15       0.03       0.18
##  [7]       0.07       0.86       0.03       0.52       0.04
##  [1] -391857.40       0.63       0.19       0.15       0.04       0.18
##  [7]       0.07       0.86       0.03       0.53       0.04
##  [1] -391790.60       0.63       0.18       0.14       0.04       0.18
##  [7]       0.07       0.85       0.03       0.53       0.04
##  [1] -391754.53       0.63       0.18       0.14       0.05       0.18
##  [7]       0.07       0.85       0.04       0.53       0.04
##  [1] -391728.88       0.63       0.18       0.14       0.05       0.18
##  [7]       0.07       0.85       0.04       0.54       0.04
##  [1] -391705.90       0.62       0.17       0.14       0.06       0.18
##  [7]       0.07       0.85       0.04       0.54       0.04
##  [1] -391682.67       0.62       0.17       0.14       0.06       0.18
##  [7]       0.07       0.85       0.04       0.54       0.04
##  [1] -391656.61       0.61       0.17       0.15       0.07       0.18
##  [7]       0.07       0.85       0.04       0.54       0.04
##  [1] -391627.05       0.61       0.18       0.15       0.07       0.18
##  [7]       0.07       0.85       0.04       0.54       0.04
##  [1] -391594.02       0.60       0.18       0.15       0.08       0.18
##  [7]       0.07       0.85       0.04       0.55       0.04
##  [1] -391557.97       0.59       0.18       0.15       0.08       0.17
##  [7]       0.07       0.85       0.04       0.55       0.04
##  [1] -391519.20       0.59       0.18       0.15       0.08       0.17
##  [7]       0.06       0.85       0.04       0.55       0.05
##  [1] -391478.70       0.58       0.18       0.15       0.09       0.17
##  [7]       0.06       0.85       0.04       0.55       0.05
##  [1] -391436.85       0.57       0.18       0.15       0.09       0.17
##  [7]       0.06       0.85       0.04       0.55       0.05
##  [1] -391395.22       0.57       0.18       0.15       0.10       0.17
##  [7]       0.06       0.85       0.04       0.55       0.05
##  [1] -391353.56       0.56       0.18       0.16       0.10       0.17
##  [7]       0.06       0.85       0.04       0.55       0.05
##  [1] -391313.67       0.55       0.19       0.16       0.11       0.17
##  [7]       0.06       0.85       0.04       0.55       0.05
##  [1] -391275.93       0.54       0.19       0.16       0.11       0.17
##  [7]       0.06       0.85       0.04       0.55       0.05
##  [1] -391240.19       0.54       0.19       0.16       0.11       0.17
##  [7]       0.06       0.85       0.04       0.55       0.06
##  [1] -391206.76       0.53       0.19       0.16       0.12       0.17
##  [7]       0.06       0.85       0.04       0.55       0.06
##  [1] -391175.85       0.52       0.19       0.16       0.12       0.17
##  [7]       0.06       0.85       0.04       0.54       0.06
##  [1] -391147.56       0.51       0.20       0.16       0.13       0.17
##  [7]       0.06       0.85       0.04       0.54       0.06
##  [1] -391121.90       0.51       0.20       0.16       0.13       0.17
##  [7]       0.06       0.85       0.04       0.54       0.06
##  [1] -391098.86       0.50       0.20       0.16       0.14       0.17
##  [7]       0.06       0.85       0.04       0.54       0.06
##  [1] -391078.34       0.49       0.20       0.17       0.14       0.17
##  [7]       0.06       0.85       0.04       0.54       0.06
##  [1] -391058.86       0.48       0.20       0.17       0.15       0.17
##  [7]       0.06       0.85       0.04       0.54       0.07
##  [1] -391042.37       0.48       0.20       0.17       0.15       0.17
##  [7]       0.06       0.85       0.04       0.54       0.07
##  [1] -391028.36       0.47       0.21       0.17       0.16       0.17
##  [7]       0.06       0.85       0.04       0.54       0.07
##  [1] -391016.45       0.46       0.21       0.17       0.16       0.17
##  [7]       0.06       0.85       0.04       0.54       0.07
##  [1] -391004.70       0.45       0.21       0.17       0.17       0.17
##  [7]       0.06       0.85       0.04       0.54       0.07
##  [1] -390996.07       0.45       0.21       0.17       0.17       0.17
##  [7]       0.06       0.86       0.04       0.54       0.07
## [1] 12
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -400398.93       0.58       0.22       0.18       0.02       0.16
##  [7]       0.08       0.87       0.03       0.51       0.05
##  [1] -392994.09       0.61       0.20       0.16       0.03       0.17
##  [7]       0.08       0.86       0.03       0.52       0.04
##  [1] -392346.60       0.63       0.19       0.15       0.03       0.18
##  [7]       0.08       0.86       0.03       0.52       0.04
##  [1] -392164.50       0.64       0.18       0.14       0.04       0.18
##  [7]       0.08       0.85       0.03       0.53       0.04
##  [1] -392090.16       0.64       0.17       0.14       0.05       0.18
##  [7]       0.08       0.85       0.03       0.53       0.04
##  [1] -392050.33       0.64       0.17       0.14       0.05       0.19
##  [7]       0.08       0.85       0.04       0.54       0.04
##  [1] -392022.23       0.64       0.17       0.14       0.06       0.19
##  [7]       0.08       0.85       0.04       0.54       0.04
##  [1] -391997.27       0.63       0.17       0.14       0.06       0.18
##  [7]       0.08       0.85       0.04       0.54       0.04
##  [1] -391972.55       0.63       0.17       0.14       0.07       0.18
##  [7]       0.08       0.85       0.04       0.54       0.04
##  [1] -391945.82       0.62       0.17       0.14       0.07       0.18
##  [7]       0.08       0.85       0.04       0.54       0.04
##  [1] -391916.61       0.61       0.17       0.14       0.08       0.18
##  [7]       0.08       0.85       0.04       0.55       0.04
##  [1] -391884.90       0.61       0.17       0.14       0.08       0.18
##  [7]       0.08       0.85       0.04       0.55       0.04
##  [1] -391851.37       0.60       0.17       0.14       0.09       0.18
##  [7]       0.07       0.85       0.04       0.55       0.04
##  [1] -391815.84       0.59       0.17       0.15       0.09       0.18
##  [7]       0.07       0.85       0.04       0.55       0.04
##  [1] -391779.28       0.58       0.17       0.15       0.09       0.18
##  [7]       0.07       0.85       0.04       0.55       0.04
##  [1] -391741.62       0.58       0.18       0.15       0.10       0.18
##  [7]       0.07       0.85       0.04       0.55       0.05
##  [1] -391704.48       0.57       0.18       0.15       0.10       0.18
##  [7]       0.07       0.85       0.04       0.55       0.05
##  [1] -391666.96       0.56       0.18       0.15       0.11       0.18
##  [7]       0.07       0.85       0.04       0.55       0.05
##  [1] -391631.57       0.55       0.18       0.15       0.11       0.18
##  [7]       0.07       0.85       0.04       0.55       0.05
##  [1] -391598.07       0.55       0.18       0.15       0.12       0.18
##  [7]       0.07       0.85       0.04       0.55       0.05
##  [1] -391566.28       0.54       0.19       0.15       0.12       0.18
##  [7]       0.07       0.85       0.04       0.55       0.05
##  [1] -391536.59       0.53       0.19       0.16       0.13       0.18
##  [7]       0.07       0.85       0.04       0.55       0.05
##  [1] -391509.12       0.52       0.19       0.16       0.13       0.18
##  [7]       0.07       0.85       0.04       0.55       0.06
##  [1] -391483.96       0.52       0.19       0.16       0.13       0.17
##  [7]       0.07       0.85       0.04       0.55       0.06
##  [1] -391461.14       0.51       0.19       0.16       0.14       0.17
##  [7]       0.07       0.85       0.04       0.55       0.06
##  [1] -391440.66       0.50       0.20       0.16       0.14       0.17
##  [7]       0.07       0.85       0.04       0.55       0.06
##  [1] -391422.48       0.49       0.20       0.16       0.15       0.17
##  [7]       0.07       0.85       0.04       0.55       0.06
##  [1] -391406.56       0.48       0.20       0.16       0.15       0.17
##  [7]       0.07       0.85       0.04       0.55       0.06
##  [1] -391392.80       0.48       0.20       0.16       0.16       0.17
##  [7]       0.07       0.85       0.04       0.55       0.06
##  [1] -391381.12       0.47       0.20       0.17       0.16       0.17
##  [7]       0.07       0.85       0.04       0.55       0.07
##  [1] -391371.06       0.46       0.20       0.17       0.17       0.17
##  [7]       0.07       0.85       0.04       0.55       0.07
##  [1] -391360.75       0.45       0.21       0.17       0.17       0.17
##  [7]       0.07       0.85       0.04       0.54       0.07
##  [1] -391353.90       0.44       0.21       0.17       0.18       0.17
##  [7]       0.07       0.85       0.04       0.54       0.07
## [1] 13
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403138.89       0.59       0.23       0.16       0.02       0.16
##  [7]       0.08       0.86       0.03       0.51       0.05
##  [1] -393726.11       0.63       0.20       0.14       0.03       0.17
##  [7]       0.08       0.85       0.03       0.52       0.05
##  [1] -392454.83       0.65       0.19       0.13       0.03       0.18
##  [7]       0.08       0.83       0.03       0.53       0.04
##  [1] -392029.12       0.65       0.18       0.13       0.04       0.18
##  [7]       0.08       0.83       0.04       0.54       0.04
##  [1] -391881.03       0.65       0.18       0.13       0.05       0.18
##  [7]       0.08       0.82       0.04       0.54       0.04
##  [1] -391849.05       0.65       0.17       0.13       0.05       0.18
##  [7]       0.08       0.82       0.04       0.54       0.04
##  [1] -391863.32       0.64       0.17       0.13       0.06       0.18
##  [7]       0.08       0.81       0.04       0.55       0.04
##  [1] -391889.93       0.63       0.17       0.13       0.06       0.18
##  [7]       0.07       0.81       0.04       0.55       0.04
##  [1] -391911.78       0.62       0.17       0.13       0.07       0.18
##  [7]       0.07       0.81       0.04       0.55       0.04
##  [1] -391921.40       0.61       0.17       0.14       0.07       0.18
##  [7]       0.07       0.81       0.04       0.55       0.04
## [1] 14
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403611.87       0.60       0.22       0.16       0.02       0.16
##  [7]       0.08       0.86       0.03       0.51       0.05
##  [1] -393996.17       0.64       0.20       0.13       0.03       0.18
##  [7]       0.08       0.85       0.03       0.52       0.04
##  [1] -392661.94       0.65       0.19       0.12       0.04       0.18
##  [7]       0.08       0.83       0.04       0.53       0.04
##  [1] -392206.40       0.66       0.18       0.12       0.04       0.19
##  [7]       0.08       0.83       0.04       0.53       0.04
##  [1] -392045.57       0.66       0.17       0.12       0.05       0.19
##  [7]       0.08       0.82       0.04       0.54       0.04
##  [1] -392008.21       0.65       0.17       0.12       0.06       0.19
##  [7]       0.08       0.81       0.04       0.54       0.04
##  [1] -392020.53       0.64       0.17       0.12       0.06       0.19
##  [7]       0.08       0.81       0.04       0.54       0.04
##  [1] -392046.43       0.64       0.17       0.13       0.07       0.19
##  [7]       0.08       0.81       0.04       0.55       0.04
##  [1] -392067.83       0.63       0.17       0.13       0.07       0.19
##  [7]       0.08       0.80       0.04       0.55       0.04
##  [1] -392077.62       0.62       0.17       0.13       0.08       0.19
##  [7]       0.08       0.80       0.04       0.55       0.04
## [1] 15
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403588.34       0.60       0.24       0.14       0.02       0.16
##  [7]       0.08       0.86       0.03       0.51       0.05
##  [1] -394220.97       0.64       0.22       0.12       0.03       0.18
##  [7]       0.08       0.85       0.03       0.52       0.04
##  [1] -393021.13       0.65       0.20       0.11       0.04       0.18
##  [7]       0.08       0.83       0.04       0.52       0.04
##  [1] -392593.88       0.66       0.20       0.10       0.04       0.19
##  [7]       0.08       0.83       0.04       0.53       0.04
##  [1] -392423.11       0.66       0.19       0.10       0.05       0.19
##  [7]       0.08       0.82       0.04       0.53       0.04
##  [1] -392365.42       0.65       0.19       0.10       0.06       0.19
##  [7]       0.08       0.81       0.04       0.54       0.04
##  [1] -392358.77       0.65       0.19       0.10       0.06       0.19
##  [7]       0.08       0.81       0.04       0.54       0.04
## [1] 16
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403501.55       0.60       0.23       0.15       0.02       0.16
##  [7]       0.08       0.86       0.03       0.51       0.05
##  [1] -394218.47       0.64       0.21       0.12       0.03       0.18
##  [7]       0.08       0.85       0.03       0.52       0.04
##  [1] -393033.25       0.65       0.20       0.11       0.04       0.19
##  [7]       0.08       0.84       0.04       0.52       0.04
##  [1] -392617.32       0.66       0.19       0.10       0.04       0.19
##  [7]       0.08       0.83       0.04       0.53       0.04
##  [1] -392452.85       0.66       0.19       0.10       0.05       0.19
##  [7]       0.08       0.82       0.04       0.53       0.04
##  [1] -392398.02       0.65       0.19       0.10       0.06       0.19
##  [7]       0.08       0.82       0.04       0.54       0.04
##  [1] -392392.35       0.65       0.19       0.10       0.06       0.19
##  [7]       0.08       0.81       0.04       0.54       0.04
## [1] 17
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -399928.06       0.57       0.19       0.22       0.02       0.16
##  [7]       0.09       0.87       0.03       0.51       0.05
##  [1] -392356.74       0.61       0.15       0.21       0.03       0.18
##  [7]       0.09       0.86       0.03       0.53       0.05
##  [1] -391316.08       0.63       0.14       0.20       0.03       0.19
##  [7]       0.09       0.85       0.03       0.54       0.04
##  [1] -390938.56       0.63       0.12       0.20       0.04       0.20
##  [7]       0.10       0.85       0.03       0.54       0.04
##  [1] -390775.20       0.63       0.12       0.20       0.04       0.20
##  [7]       0.10       0.85       0.03       0.55       0.04
##  [1] -390704.67       0.63       0.11       0.21       0.05       0.20
##  [7]       0.10       0.84       0.04       0.56       0.04
##  [1] -390676.38       0.63       0.11       0.21       0.05       0.21
##  [7]       0.10       0.84       0.04       0.56       0.04
##  [1] -390665.19       0.62       0.11       0.21       0.06       0.21
##  [7]       0.10       0.84       0.04       0.56       0.04
##  [1] -390658.34       0.61       0.11       0.21       0.06       0.21
##  [7]       0.10       0.84       0.04       0.56       0.04
## [1] 18
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -398969.63       0.57       0.18       0.23       0.02       0.16
##  [7]       0.09       0.87       0.03       0.51       0.05
##  [1] -392350.42       0.61       0.15       0.22       0.03       0.18
##  [7]       0.09       0.86       0.03       0.53       0.04
##  [1] -391393.38       0.63       0.13       0.21       0.03       0.19
##  [7]       0.10       0.86       0.03       0.54       0.04
##  [1] -391026.20       0.63       0.12       0.21       0.04       0.20
##  [7]       0.10       0.85       0.03       0.54       0.04
##  [1] -390857.04       0.63       0.11       0.21       0.04       0.20
##  [7]       0.11       0.85       0.04       0.55       0.04
##  [1] -390775.81       0.63       0.11       0.21       0.05       0.20
##  [7]       0.11       0.85       0.04       0.56       0.04
##  [1] -390735.21       0.63       0.11       0.21       0.05       0.21
##  [7]       0.11       0.85       0.04       0.56       0.04
##  [1] -390711.63       0.62       0.10       0.21       0.06       0.21
##  [7]       0.11       0.85       0.04       0.56       0.04
##  [1] -390692.85       0.62       0.10       0.22       0.06       0.21
##  [7]       0.11       0.85       0.04       0.56       0.04
##  [1] -390673.80       0.61       0.10       0.22       0.07       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390651.64       0.61       0.10       0.22       0.07       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390625.77       0.60       0.11       0.22       0.07       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390596.83       0.59       0.11       0.22       0.08       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390565.71       0.59       0.11       0.22       0.08       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390533.05       0.58       0.11       0.22       0.09       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390499.48       0.58       0.11       0.22       0.09       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390465.59       0.57       0.11       0.22       0.09       0.21
##  [7]       0.11       0.85       0.04       0.57       0.04
##  [1] -390431.78       0.56       0.12       0.23       0.10       0.20
##  [7]       0.11       0.85       0.04       0.58       0.05
##  [1] -390398.38       0.56       0.12       0.23       0.10       0.20
##  [7]       0.11       0.85       0.04       0.58       0.05
##  [1] -390365.66       0.55       0.12       0.23       0.10       0.20
##  [7]       0.11       0.85       0.04       0.58       0.05
##  [1] -390333.75       0.55       0.12       0.23       0.11       0.20
##  [7]       0.10       0.85       0.04       0.58       0.05
##  [1] -390302.78       0.54       0.12       0.23       0.11       0.20
##  [7]       0.10       0.85       0.04       0.58       0.05
##  [1] -390272.89       0.53       0.13       0.23       0.11       0.20
##  [7]       0.10       0.85       0.04       0.58       0.05
##  [1] -390244.14       0.53       0.13       0.23       0.12       0.20
##  [7]       0.10       0.85       0.04       0.58       0.05
##  [1] -390216.59       0.52       0.13       0.23       0.12       0.20
##  [7]       0.10       0.85       0.04       0.58       0.05
##  [1] -390190.28       0.51       0.13       0.23       0.12       0.20
##  [7]       0.10       0.85       0.04       0.58       0.05
##  [1] -390165.23       0.51       0.13       0.23       0.13       0.20
##  [7]       0.10       0.85       0.04       0.58       0.05
##  [1] -390141.49       0.50       0.14       0.23       0.13       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -390118.97       0.50       0.14       0.23       0.13       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -390097.75       0.49       0.14       0.23       0.14       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -390077.78       0.48       0.14       0.23       0.14       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -390059.02       0.48       0.14       0.23       0.14       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -390041.47       0.47       0.15       0.23       0.15       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -390025.10       0.46       0.15       0.24       0.15       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -390009.88       0.46       0.15       0.24       0.16       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -389995.77       0.45       0.15       0.24       0.16       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -389982.74       0.45       0.15       0.24       0.16       0.20
##  [7]       0.10       0.85       0.04       0.58       0.06
##  [1] -389970.76       0.44       0.16       0.24       0.17       0.20
##  [7]       0.10       0.85       0.04       0.58       0.07
##  [1] -389959.79       0.43       0.16       0.24       0.17       0.20
##  [7]       0.10       0.85       0.04       0.58       0.07
##  [1] -389949.80       0.43       0.16       0.24       0.17       0.20
##  [7]       0.10       0.85       0.04       0.58       0.07
## [1] 19
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -399597.90       0.57       0.21       0.21       0.02       0.16
##  [7]       0.08       0.87       0.03       0.51       0.05
##  [1] -392507.68       0.61       0.18       0.19       0.03       0.17
##  [7]       0.08       0.86       0.03       0.52       0.05
##  [1] -391710.23       0.62       0.16       0.18       0.03       0.18
##  [7]       0.08       0.86       0.03       0.53       0.04
##  [1] -391450.54       0.63       0.15       0.18       0.04       0.18
##  [7]       0.08       0.85       0.03       0.54       0.04
##  [1] -391342.43       0.63       0.15       0.18       0.04       0.18
##  [7]       0.09       0.85       0.03       0.54       0.04
##  [1] -391295.44       0.63       0.14       0.18       0.05       0.19
##  [7]       0.09       0.85       0.03       0.55       0.04
##  [1] -391276.18       0.63       0.14       0.18       0.05       0.19
##  [7]       0.09       0.85       0.04       0.55       0.04
##  [1] -391269.00       0.62       0.14       0.18       0.06       0.18
##  [7]       0.08       0.85       0.04       0.56       0.04
## [1] 20
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -400914.74       0.58       0.20       0.20       0.02       0.16
##  [7]       0.08       0.87       0.03       0.51       0.05
##  [1] -392712.31       0.62       0.18       0.18       0.03       0.18
##  [7]       0.08       0.86       0.03       0.52       0.04
##  [1] -391819.32       0.63       0.16       0.17       0.03       0.19
##  [7]       0.08       0.85       0.03       0.53       0.04
##  [1] -391531.20       0.64       0.15       0.17       0.04       0.19
##  [7]       0.08       0.85       0.03       0.54       0.04
##  [1] -391407.01       0.64       0.15       0.17       0.05       0.20
##  [7]       0.08       0.85       0.03       0.54       0.04
##  [1] -391347.36       0.64       0.14       0.17       0.05       0.20
##  [7]       0.08       0.85       0.03       0.55       0.04
##  [1] -391316.93       0.63       0.14       0.17       0.06       0.20
##  [7]       0.08       0.84       0.03       0.55       0.04
##  [1] -391299.60       0.63       0.14       0.17       0.06       0.20
##  [7]       0.08       0.84       0.03       0.56       0.04
##  [1] -391287.10       0.62       0.14       0.17       0.07       0.20
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391275.59       0.61       0.14       0.17       0.07       0.20
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391262.07       0.61       0.15       0.17       0.08       0.20
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391245.40       0.60       0.15       0.17       0.08       0.20
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391225.64       0.59       0.15       0.18       0.09       0.20
##  [7]       0.08       0.84       0.04       0.56       0.04
##  [1] -391203.00       0.58       0.15       0.18       0.09       0.20
##  [7]       0.08       0.84       0.04       0.57       0.04
##  [1] -391177.94       0.57       0.15       0.18       0.09       0.20
##  [7]       0.08       0.84       0.04       0.57       0.04
##  [1] -391152.52       0.57       0.16       0.18       0.10       0.20
##  [7]       0.08       0.84       0.04       0.57       0.04
##  [1] -391123.76       0.56       0.16       0.18       0.10       0.20
##  [7]       0.08       0.84       0.04       0.57       0.04
##  [1] -391094.77       0.55       0.16       0.18       0.11       0.20
##  [7]       0.08       0.84       0.04       0.57       0.05
##  [1] -391065.76       0.54       0.17       0.18       0.11       0.20
##  [7]       0.08       0.84       0.04       0.57       0.05
##  [1] -391037.17       0.53       0.17       0.19       0.11       0.20
##  [7]       0.08       0.84       0.04       0.57       0.05
##  [1] -391009.32       0.52       0.17       0.19       0.12       0.20
##  [7]       0.08       0.84       0.04       0.57       0.05
##  [1] -390982.50       0.52       0.17       0.19       0.12       0.20
##  [7]       0.08       0.84       0.04       0.57       0.05
##  [1] -390956.89       0.51       0.18       0.19       0.13       0.20
##  [7]       0.08       0.84       0.04       0.57       0.05
##  [1] -390932.64       0.50       0.18       0.19       0.13       0.20
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390909.87       0.49       0.18       0.19       0.14       0.20
##  [7]       0.08       0.85       0.04       0.57       0.05
##  [1] -390888.60       0.48       0.19       0.19       0.14       0.20
##  [7]       0.08       0.85       0.03       0.57       0.05
##  [1] -390868.86       0.47       0.19       0.19       0.14       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390850.63       0.47       0.19       0.19       0.15       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390833.89       0.46       0.19       0.20       0.15       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390818.59       0.45       0.20       0.20       0.16       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390804.67       0.44       0.20       0.20       0.16       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390792.09       0.43       0.20       0.20       0.17       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390780.76       0.42       0.20       0.20       0.17       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390770.64       0.42       0.21       0.20       0.18       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
##  [1] -390761.67       0.41       0.21       0.20       0.18       0.20
##  [7]       0.08       0.85       0.03       0.57       0.06
## [1] 21
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403647.99       0.60       0.24       0.14       0.02       0.16
##  [7]       0.08       0.86       0.03       0.51       0.05
##  [1] -393801.07       0.64       0.22       0.12       0.03       0.17
##  [7]       0.08       0.84       0.03       0.52       0.04
##  [1] -392537.71       0.65       0.21       0.11       0.04       0.18
##  [7]       0.08       0.83       0.03       0.53       0.04
##  [1] -392095.16       0.65       0.20       0.10       0.04       0.18
##  [7]       0.08       0.82       0.03       0.53       0.04
##  [1] -391922.77       0.65       0.19       0.10       0.05       0.18
##  [7]       0.08       0.81       0.03       0.54       0.04
##  [1] -391869.92       0.65       0.19       0.10       0.06       0.18
##  [7]       0.08       0.81       0.04       0.54       0.04
##  [1] -391870.44       0.64       0.19       0.11       0.07       0.18
##  [7]       0.08       0.80       0.04       0.54       0.04
## [1] 22
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -402847.53       0.59       0.24       0.15       0.02       0.16
##  [7]       0.08       0.86       0.03       0.51       0.05
##  [1] -393886.15       0.63       0.22       0.12       0.03       0.17
##  [7]       0.07       0.85       0.03       0.52       0.04
##  [1] -392760.66       0.64       0.21       0.11       0.03       0.17
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392377.06       0.65       0.20       0.11       0.04       0.18
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392231.32       0.65       0.20       0.11       0.05       0.18
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -392186.68       0.64       0.19       0.11       0.05       0.18
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -392185.73       0.64       0.19       0.11       0.06       0.18
##  [7]       0.07       0.81       0.04       0.54       0.04
## [1] 23
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -402801.75       0.59       0.23       0.16       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393639.57       0.63       0.21       0.14       0.03       0.17
##  [7]       0.07       0.85       0.03       0.52       0.05
##  [1] -392551.37       0.64       0.20       0.13       0.03       0.18
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392180.72       0.65       0.19       0.12       0.04       0.18
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392033.78       0.65       0.19       0.12       0.05       0.18
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391983.12       0.64       0.19       0.12       0.05       0.18
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391975.93       0.64       0.18       0.12       0.06       0.18
##  [7]       0.07       0.82       0.04       0.54       0.04
## [1] 24
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -404177.72       0.60       0.23       0.15       0.02       0.17
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -394036.85       0.64       0.21       0.12       0.03       0.18
##  [7]       0.07       0.85       0.04       0.52       0.04
##  [1] -392802.68       0.65       0.20       0.11       0.04       0.19
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392371.97       0.66       0.20       0.10       0.04       0.20
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392191.99       0.65       0.19       0.10       0.05       0.20
##  [7]       0.07       0.82       0.04       0.53       0.04
##  [1] -392121.30       0.65       0.19       0.10       0.06       0.20
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -392101.50       0.64       0.19       0.10       0.06       0.20
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -392102.06       0.63       0.19       0.10       0.07       0.20
##  [7]       0.07       0.81       0.05       0.54       0.04
## [1] 25
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -404482.56       0.61       0.23       0.14       0.02       0.17
##  [7]       0.07       0.86       0.03       0.51       0.05
##  [1] -393990.92       0.64       0.21       0.12       0.03       0.18
##  [7]       0.07       0.85       0.03       0.52       0.04
##  [1] -392686.41       0.66       0.20       0.11       0.04       0.19
##  [7]       0.07       0.83       0.03       0.52       0.04
##  [1] -392220.64       0.66       0.19       0.10       0.05       0.19
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392024.59       0.66       0.19       0.10       0.05       0.20
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -391949.61       0.65       0.19       0.10       0.06       0.20
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -391931.37       0.64       0.19       0.10       0.07       0.20
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -391935.15       0.63       0.19       0.10       0.08       0.20
##  [7]       0.07       0.80       0.04       0.54       0.04
## [1] 26
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -402869.78       0.59       0.26       0.14       0.02       0.15
##  [7]       0.07       0.86       0.03       0.51       0.05
##  [1] -393897.60       0.62       0.24       0.11       0.03       0.17
##  [7]       0.07       0.85       0.03       0.52       0.05
##  [1] -392820.30       0.64       0.23       0.10       0.03       0.17
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392440.62       0.64       0.22       0.10       0.04       0.17
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392283.37       0.64       0.22       0.09       0.05       0.17
##  [7]       0.07       0.82       0.04       0.53       0.04
##  [1] -392225.56       0.64       0.22       0.09       0.05       0.17
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -392214.34       0.63       0.22       0.09       0.06       0.17
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -392221.30       0.63       0.22       0.10       0.06       0.17
##  [7]       0.07       0.81       0.04       0.54       0.04
## [1] 27
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403547.91       0.59       0.25       0.14       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393838.80       0.63       0.23       0.11       0.03       0.18
##  [7]       0.07       0.85       0.03       0.51       0.04
##  [1] -392779.46       0.64       0.22       0.10       0.03       0.18
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392404.66       0.65       0.22       0.10       0.04       0.18
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392235.20       0.65       0.21       0.09       0.05       0.18
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392157.19       0.64       0.21       0.09       0.05       0.18
##  [7]       0.07       0.82       0.04       0.53       0.04
##  [1] -392124.18       0.64       0.21       0.09       0.06       0.18
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -392111.11       0.63       0.21       0.09       0.07       0.18
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -392103.47       0.62       0.21       0.10       0.07       0.18
##  [7]       0.07       0.81       0.05       0.54       0.04
## [1] 28
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403985.93       0.60       0.25       0.14       0.02       0.16
##  [7]       0.07       0.86       0.03       0.51       0.05
##  [1] -393904.32       0.63       0.23       0.11       0.03       0.18
##  [7]       0.07       0.85       0.03       0.52       0.04
##  [1] -392759.65       0.64       0.22       0.10       0.03       0.18
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392357.65       0.65       0.22       0.09       0.04       0.19
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392183.66       0.65       0.21       0.09       0.05       0.19
##  [7]       0.07       0.82       0.04       0.53       0.04
##  [1] -392111.90       0.64       0.21       0.09       0.06       0.19
##  [7]       0.07       0.82       0.04       0.53       0.04
##  [1] -392090.00       0.64       0.21       0.09       0.06       0.19
##  [7]       0.07       0.81       0.04       0.54       0.04
##  [1] -392089.45       0.63       0.21       0.09       0.07       0.19
##  [7]       0.07       0.81       0.04       0.54       0.04
## [1] 29
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -402127.58       0.58       0.25       0.15       0.02       0.15
##  [7]       0.08       0.87       0.03       0.51       0.05
##  [1] -393953.50       0.62       0.24       0.12       0.03       0.17
##  [7]       0.07       0.85       0.04       0.52       0.05
##  [1] -392980.52       0.64       0.22       0.11       0.03       0.17
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392629.74       0.64       0.22       0.10       0.04       0.17
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392477.38       0.64       0.21       0.10       0.05       0.17
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392413.92       0.64       0.21       0.10       0.05       0.17
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -392392.53       0.64       0.21       0.10       0.06       0.17
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -392388.13       0.63       0.21       0.10       0.06       0.17
##  [7]       0.07       0.82       0.04       0.54       0.04
## [1] 30
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403506.10       0.60       0.24       0.14       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -394385.31       0.63       0.22       0.11       0.03       0.18
##  [7]       0.07       0.85       0.04       0.52       0.04
##  [1] -393241.12       0.65       0.21       0.10       0.04       0.18
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392817.30       0.65       0.21       0.10       0.04       0.19
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392632.00       0.65       0.20       0.09       0.05       0.19
##  [7]       0.07       0.82       0.04       0.53       0.04
##  [1] -392557.26       0.65       0.20       0.09       0.06       0.19
##  [7]       0.07       0.82       0.05       0.54       0.04
##  [1] -392536.92       0.65       0.20       0.09       0.06       0.19
##  [7]       0.07       0.81       0.05       0.54       0.04
##  [1] -392540.01       0.64       0.20       0.09       0.07       0.19
##  [7]       0.07       0.81       0.05       0.54       0.04
## [1] 31
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403240.20       0.59       0.23       0.16       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393403.63       0.63       0.21       0.14       0.03       0.18
##  [7]       0.07       0.85       0.03       0.52       0.05
##  [1] -392255.93       0.64       0.19       0.13       0.03       0.18
##  [7]       0.07       0.84       0.03       0.53       0.04
##  [1] -391885.38       0.64       0.19       0.13       0.04       0.19
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -391746.01       0.64       0.18       0.13       0.05       0.19
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391699.79       0.64       0.18       0.13       0.05       0.19
##  [7]       0.07       0.82       0.04       0.54       0.04
##  [1] -391693.22       0.63       0.18       0.13       0.06       0.19
##  [7]       0.07       0.82       0.04       0.54       0.04
## [1] 32
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -402911.87       0.59       0.23       0.17       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393714.80       0.62       0.21       0.14       0.03       0.18
##  [7]       0.07       0.85       0.04       0.52       0.05
##  [1] -392592.72       0.64       0.19       0.13       0.03       0.18
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392230.87       0.65       0.19       0.13       0.04       0.19
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392097.95       0.65       0.18       0.13       0.04       0.19
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392055.26       0.64       0.18       0.13       0.05       0.19
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -392049.02       0.64       0.18       0.13       0.05       0.19
##  [7]       0.07       0.82       0.04       0.54       0.04
## [1] 33
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -403904.05       0.59       0.20       0.18       0.02       0.18
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393101.84       0.63       0.19       0.16       0.03       0.20
##  [7]       0.06       0.86       0.04       0.51       0.05
##  [1] -391934.01       0.64       0.18       0.15       0.03       0.21
##  [7]       0.06       0.85       0.04       0.52       0.05
##  [1] -391592.67       0.64       0.18       0.14       0.04       0.22
##  [7]       0.06       0.85       0.04       0.52       0.05
##  [1] -391470.08       0.64       0.18       0.14       0.04       0.22
##  [7]       0.06       0.84       0.04       0.53       0.04
##  [1] -391426.83       0.63       0.18       0.14       0.05       0.22
##  [7]       0.06       0.84       0.04       0.53       0.04
##  [1] -391416.24       0.63       0.18       0.15       0.05       0.22
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -391418.69       0.62       0.18       0.15       0.06       0.22
##  [7]       0.06       0.83       0.05       0.54       0.04
## [1] 34
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -401732.65       0.57       0.26       0.15       0.02       0.15
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393375.68       0.61       0.24       0.12       0.03       0.16
##  [7]       0.07       0.85       0.03       0.51       0.04
##  [1] -392550.12       0.63       0.23       0.11       0.03       0.17
##  [7]       0.07       0.85       0.04       0.52       0.04
##  [1] -392288.08       0.63       0.22       0.11       0.04       0.17
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392178.39       0.63       0.22       0.10       0.04       0.17
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392127.30       0.63       0.22       0.10       0.05       0.17
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392100.32       0.63       0.22       0.10       0.05       0.17
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -392081.06       0.62       0.21       0.10       0.06       0.16
##  [7]       0.06       0.83       0.04       0.53       0.04
##  [1] -392061.05       0.62       0.21       0.10       0.06       0.16
##  [7]       0.06       0.82       0.04       0.53       0.04
##  [1] -392035.34       0.61       0.22       0.10       0.07       0.16
##  [7]       0.06       0.82       0.04       0.54       0.04
##  [1] -392002.17       0.60       0.22       0.11       0.07       0.16
##  [7]       0.06       0.82       0.04       0.54       0.04
##  [1] -391961.38       0.60       0.22       0.11       0.08       0.16
##  [7]       0.06       0.82       0.04       0.53       0.04
##  [1] -391913.76       0.59       0.22       0.11       0.08       0.16
##  [7]       0.06       0.82       0.04       0.53       0.04
##  [1] -391860.69       0.58       0.22       0.11       0.09       0.16
##  [7]       0.06       0.82       0.04       0.53       0.05
##  [1] -391803.96       0.58       0.22       0.11       0.09       0.16
##  [7]       0.06       0.82       0.04       0.53       0.05
##  [1] -391744.88       0.57       0.22       0.11       0.09       0.16
##  [7]       0.06       0.82       0.04       0.53       0.05
##  [1] -391685.00       0.56       0.22       0.12       0.10       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391625.54       0.55       0.22       0.12       0.10       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391567.42       0.55       0.23       0.12       0.11       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391511.57       0.54       0.23       0.12       0.11       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391458.00       0.53       0.23       0.12       0.12       0.16
##  [7]       0.06       0.82       0.05       0.53       0.06
##  [1] -391407.30       0.52       0.23       0.12       0.12       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391359.62       0.52       0.23       0.13       0.12       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391314.99       0.51       0.23       0.13       0.13       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391273.38       0.50       0.24       0.13       0.13       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391234.68       0.49       0.24       0.13       0.14       0.15
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391198.76       0.49       0.24       0.13       0.14       0.15
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391165.49       0.48       0.24       0.14       0.15       0.15
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391134.70       0.47       0.24       0.14       0.15       0.15
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -391106.23       0.46       0.24       0.14       0.16       0.15
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -391079.92       0.45       0.24       0.14       0.16       0.15
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -391055.63       0.45       0.25       0.14       0.17       0.15
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -391033.23       0.44       0.25       0.15       0.17       0.15
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -391012.57       0.43       0.25       0.15       0.18       0.15
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -390993.55       0.42       0.25       0.15       0.18       0.15
##  [7]       0.05       0.82       0.05       0.51       0.07
##  [1] -390976.05       0.41       0.25       0.15       0.18       0.15
##  [7]       0.05       0.82       0.05       0.51       0.07
##  [1] -390959.97       0.41       0.25       0.15       0.19       0.15
##  [7]       0.05       0.82       0.05       0.51       0.08
##  [1] -390945.22       0.40       0.25       0.15       0.19       0.15
##  [7]       0.05       0.82       0.05       0.51       0.08
##  [1] -390931.72       0.39       0.25       0.16       0.20       0.15
##  [7]       0.05       0.82       0.05       0.51       0.08
##  [1] -390919.39       0.38       0.25       0.16       0.20       0.15
##  [7]       0.05       0.82       0.05       0.50       0.08
##  [1] -390908.16       0.38       0.26       0.16       0.21       0.15
##  [7]       0.05       0.82       0.05       0.50       0.08
##  [1] -390897.97       0.37       0.26       0.16       0.21       0.15
##  [7]       0.05       0.82       0.05       0.50       0.08
##  [1] -390888.75       0.36       0.26       0.16       0.22       0.15
##  [7]       0.05       0.82       0.05       0.50       0.08
## [1] 35
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -401850.66       0.57       0.25       0.16       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393221.70       0.61       0.23       0.13       0.03       0.17
##  [7]       0.07       0.86       0.03       0.52       0.05
##  [1] -392372.99       0.62       0.22       0.12       0.03       0.17
##  [7]       0.07       0.85       0.04       0.52       0.04
##  [1] -392119.38       0.63       0.22       0.12       0.04       0.17
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392022.92       0.63       0.21       0.12       0.04       0.17
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -391985.13       0.63       0.21       0.11       0.05       0.17
##  [7]       0.07       0.83       0.04       0.53       0.04
##  [1] -391970.90       0.63       0.21       0.11       0.05       0.17
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -391964.31       0.62       0.21       0.12       0.06       0.17
##  [7]       0.06       0.83       0.04       0.54       0.04
## [1] 36
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -401823.48       0.57       0.25       0.15       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393352.60       0.61       0.24       0.12       0.03       0.17
##  [7]       0.07       0.86       0.04       0.51       0.04
##  [1] -392519.40       0.62       0.23       0.11       0.03       0.17
##  [7]       0.07       0.85       0.04       0.52       0.04
##  [1] -392268.86       0.63       0.23       0.11       0.04       0.17
##  [7]       0.07       0.84       0.04       0.52       0.04
##  [1] -392172.95       0.63       0.22       0.10       0.04       0.17
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392134.47       0.63       0.22       0.10       0.05       0.17
##  [7]       0.06       0.83       0.04       0.53       0.04
##  [1] -392118.38       0.63       0.22       0.10       0.05       0.17
##  [7]       0.06       0.83       0.04       0.53       0.04
##  [1] -392108.20       0.62       0.22       0.10       0.06       0.17
##  [7]       0.06       0.83       0.04       0.53       0.04
##  [1] -392095.12       0.62       0.22       0.10       0.06       0.17
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -392074.93       0.61       0.22       0.11       0.07       0.16
##  [7]       0.06       0.82       0.04       0.54       0.04
##  [1] -392046.15       0.60       0.22       0.11       0.07       0.16
##  [7]       0.06       0.82       0.04       0.54       0.04
##  [1] -392008.87       0.60       0.22       0.11       0.08       0.16
##  [7]       0.06       0.82       0.04       0.54       0.04
##  [1] -391964.11       0.59       0.22       0.11       0.08       0.16
##  [7]       0.06       0.82       0.04       0.53       0.04
##  [1] -391913.38       0.58       0.22       0.11       0.09       0.16
##  [7]       0.06       0.82       0.04       0.53       0.04
##  [1] -391858.64       0.58       0.22       0.11       0.09       0.16
##  [7]       0.06       0.82       0.04       0.53       0.04
##  [1] -391801.12       0.57       0.22       0.11       0.09       0.16
##  [7]       0.06       0.82       0.04       0.53       0.05
##  [1] -391742.47       0.56       0.22       0.12       0.10       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391683.95       0.55       0.23       0.12       0.10       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391626.52       0.55       0.23       0.12       0.11       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391571.13       0.54       0.23       0.12       0.11       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391517.83       0.53       0.23       0.12       0.11       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391467.22       0.52       0.23       0.13       0.12       0.16
##  [7]       0.06       0.82       0.05       0.53       0.05
##  [1] -391419.47       0.52       0.23       0.13       0.12       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391374.65       0.51       0.24       0.13       0.13       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391332.73       0.50       0.24       0.13       0.13       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391293.63       0.49       0.24       0.13       0.13       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391257.24       0.49       0.24       0.13       0.14       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391223.42       0.48       0.24       0.14       0.14       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391192.01       0.47       0.24       0.14       0.15       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391162.88       0.46       0.25       0.14       0.15       0.16
##  [7]       0.06       0.82       0.05       0.52       0.06
##  [1] -391135.87       0.46       0.25       0.14       0.16       0.16
##  [7]       0.06       0.82       0.05       0.52       0.07
##  [1] -391110.84       0.45       0.25       0.14       0.16       0.16
##  [7]       0.06       0.82       0.05       0.52       0.07
##  [1] -391087.66       0.44       0.25       0.15       0.16       0.16
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -391066.18       0.43       0.25       0.15       0.17       0.16
##  [7]       0.06       0.82       0.05       0.51       0.07
##  [1] -391046.31       0.43       0.25       0.15       0.17       0.15
##  [7]       0.05       0.82       0.05       0.51       0.07
##  [1] -391027.93       0.42       0.25       0.15       0.18       0.15
##  [7]       0.05       0.82       0.05       0.51       0.07
##  [1] -391010.93       0.41       0.25       0.15       0.18       0.15
##  [7]       0.05       0.82       0.05       0.51       0.07
##  [1] -390995.24       0.40       0.26       0.15       0.19       0.15
##  [7]       0.05       0.82       0.05       0.51       0.07
##  [1] -390980.76       0.40       0.26       0.16       0.19       0.15
##  [7]       0.05       0.82       0.05       0.51       0.07
##  [1] -390967.43       0.39       0.26       0.16       0.20       0.15
##  [7]       0.05       0.82       0.05       0.51       0.08
##  [1] -390955.16       0.38       0.26       0.16       0.20       0.15
##  [7]       0.05       0.82       0.05       0.51       0.08
##  [1] -390943.90       0.37       0.26       0.16       0.21       0.15
##  [7]       0.05       0.82       0.05       0.51       0.08
##  [1] -390933.58       0.37       0.26       0.16       0.21       0.15
##  [7]       0.05       0.83       0.05       0.51       0.08
##  [1] -390924.16       0.36       0.26       0.16       0.21       0.15
##  [7]       0.05       0.83       0.05       0.51       0.08
## [1] 37
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -401646.97       0.58       0.23       0.17       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -392856.08       0.61       0.21       0.15       0.03       0.17
##  [7]       0.07       0.86       0.03       0.52       0.05
##  [1] -391939.60       0.63       0.20       0.14       0.03       0.17
##  [7]       0.07       0.85       0.03       0.53       0.04
##  [1] -391634.20       0.63       0.19       0.14       0.04       0.17
##  [7]       0.07       0.84       0.03       0.53       0.04
##  [1] -391506.99       0.63       0.18       0.14       0.04       0.17
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -391455.22       0.63       0.18       0.14       0.05       0.17
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -391438.02       0.63       0.18       0.14       0.05       0.17
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391434.36       0.62       0.18       0.14       0.06       0.17
##  [7]       0.07       0.83       0.04       0.55       0.04
## [1] 38
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -402091.04       0.58       0.23       0.17       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -392947.65       0.62       0.21       0.14       0.03       0.17
##  [7]       0.07       0.85       0.03       0.52       0.05
##  [1] -391982.95       0.63       0.20       0.14       0.03       0.17
##  [7]       0.07       0.84       0.03       0.53       0.04
##  [1] -391665.86       0.64       0.19       0.13       0.04       0.17
##  [7]       0.07       0.84       0.03       0.53       0.04
##  [1] -391536.11       0.64       0.19       0.13       0.04       0.17
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391485.04       0.63       0.18       0.13       0.05       0.17
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391469.83       0.63       0.18       0.13       0.06       0.17
##  [7]       0.07       0.83       0.04       0.54       0.04
##  [1] -391468.32       0.62       0.18       0.14       0.06       0.17
##  [7]       0.07       0.83       0.04       0.55       0.04
## [1] 39
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -400190.16       0.56       0.24       0.18       0.02       0.15
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -392404.48       0.59       0.22       0.16       0.02       0.16
##  [7]       0.07       0.86       0.03       0.52       0.05
##  [1] -391577.56       0.61       0.21       0.16       0.03       0.16
##  [7]       0.07       0.85       0.03       0.53       0.05
##  [1] -391319.07       0.62       0.20       0.15       0.03       0.16
##  [7]       0.07       0.85       0.03       0.54       0.04
##  [1] -391227.25       0.62       0.19       0.15       0.04       0.16
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -391205.47       0.62       0.19       0.15       0.04       0.16
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -391214.81       0.61       0.19       0.15       0.05       0.15
##  [7]       0.06       0.84       0.04       0.55       0.04
## [1] 40
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -400741.31       0.57       0.25       0.16       0.02       0.15
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393228.22       0.61       0.23       0.13       0.03       0.16
##  [7]       0.07       0.86       0.03       0.52       0.04
##  [1] -392527.82       0.62       0.22       0.12       0.03       0.17
##  [7]       0.07       0.85       0.04       0.52       0.04
##  [1] -392307.96       0.63       0.22       0.12       0.04       0.17
##  [7]       0.07       0.85       0.04       0.53       0.04
##  [1] -392212.22       0.63       0.21       0.11       0.04       0.17
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392164.22       0.63       0.21       0.11       0.05       0.16
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392136.77       0.63       0.21       0.11       0.05       0.16
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -392117.62       0.63       0.20       0.11       0.06       0.16
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -392098.58       0.62       0.20       0.11       0.06       0.16
##  [7]       0.06       0.84       0.04       0.54       0.04
##  [1] -392075.68       0.62       0.20       0.11       0.07       0.16
##  [7]       0.06       0.84       0.04       0.54       0.04
##  [1] -392047.06       0.61       0.20       0.11       0.07       0.16
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -392012.25       0.60       0.20       0.11       0.08       0.16
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -391971.56       0.60       0.21       0.12       0.08       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391925.96       0.59       0.21       0.12       0.08       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391876.63       0.59       0.21       0.12       0.09       0.15
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391825.04       0.58       0.21       0.12       0.09       0.15
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391772.23       0.57       0.21       0.12       0.10       0.15
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391719.71       0.57       0.21       0.12       0.10       0.15
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391668.19       0.56       0.21       0.12       0.10       0.15
##  [7]       0.06       0.84       0.04       0.54       0.05
##  [1] -391618.50       0.55       0.21       0.13       0.11       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391571.22       0.55       0.21       0.13       0.11       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391526.75       0.54       0.22       0.13       0.12       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391485.32       0.53       0.22       0.13       0.12       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391447.05       0.52       0.22       0.13       0.13       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391411.95       0.52       0.22       0.13       0.13       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391379.97       0.51       0.22       0.13       0.14       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391351.01       0.50       0.22       0.13       0.14       0.15
##  [7]       0.06       0.84       0.04       0.53       0.07
##  [1] -391324.93       0.50       0.22       0.14       0.14       0.15
##  [7]       0.06       0.84       0.04       0.53       0.07
##  [1] -391301.57       0.49       0.22       0.14       0.15       0.15
##  [7]       0.06       0.84       0.04       0.52       0.07
##  [1] -391280.77       0.48       0.23       0.14       0.15       0.15
##  [7]       0.06       0.84       0.04       0.52       0.07
##  [1] -391262.36       0.47       0.23       0.14       0.16       0.15
##  [7]       0.06       0.84       0.04       0.52       0.07
##  [1] -391246.18       0.47       0.23       0.14       0.16       0.15
##  [7]       0.06       0.84       0.04       0.52       0.07
##  [1] -391232.08       0.46       0.23       0.14       0.17       0.15
##  [7]       0.05       0.84       0.04       0.52       0.07
##  [1] -391219.90       0.45       0.23       0.14       0.17       0.15
##  [7]       0.05       0.84       0.04       0.52       0.08
##  [1] -391209.51       0.45       0.23       0.14       0.18       0.15
##  [7]       0.05       0.84       0.04       0.52       0.08
##  [1] -391200.83       0.44       0.23       0.15       0.18       0.15
##  [7]       0.05       0.84       0.04       0.52       0.08
## [1] 41
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -401299.92       0.58       0.24       0.16       0.02       0.16
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393019.54       0.61       0.23       0.13       0.03       0.17
##  [7]       0.07       0.86       0.03       0.52       0.04
##  [1] -392273.34       0.63       0.21       0.12       0.03       0.17
##  [7]       0.07       0.85       0.03       0.52       0.04
##  [1] -392032.83       0.64       0.21       0.12       0.04       0.17
##  [7]       0.07       0.85       0.03       0.53       0.04
##  [1] -391924.78       0.64       0.20       0.12       0.05       0.17
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -391870.43       0.64       0.20       0.11       0.05       0.17
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -391840.92       0.63       0.20       0.11       0.06       0.17
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -391822.46       0.63       0.20       0.11       0.06       0.16
##  [7]       0.06       0.84       0.04       0.54       0.04
##  [1] -391805.34       0.62       0.20       0.12       0.07       0.16
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -391784.51       0.61       0.20       0.12       0.07       0.16
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -391757.56       0.61       0.20       0.12       0.08       0.16
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -391723.87       0.60       0.20       0.12       0.08       0.16
##  [7]       0.06       0.83       0.04       0.54       0.04
##  [1] -391683.69       0.59       0.20       0.12       0.09       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391638.31       0.58       0.20       0.12       0.09       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391588.76       0.57       0.20       0.12       0.10       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391537.02       0.57       0.20       0.13       0.10       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391484.59       0.56       0.20       0.13       0.11       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391432.83       0.55       0.21       0.13       0.11       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391382.86       0.54       0.21       0.13       0.12       0.16
##  [7]       0.06       0.83       0.04       0.54       0.05
##  [1] -391335.37       0.53       0.21       0.13       0.12       0.16
##  [7]       0.06       0.83       0.04       0.54       0.06
##  [1] -391290.96       0.53       0.21       0.13       0.13       0.15
##  [7]       0.06       0.83       0.04       0.54       0.06
##  [1] -391250.01       0.52       0.21       0.14       0.13       0.15
##  [7]       0.06       0.83       0.04       0.54       0.06
##  [1] -391212.68       0.51       0.21       0.14       0.14       0.15
##  [7]       0.06       0.83       0.04       0.54       0.06
##  [1] -391179.03       0.50       0.22       0.14       0.14       0.15
##  [7]       0.06       0.83       0.04       0.53       0.06
##  [1] -391148.98       0.49       0.22       0.14       0.15       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391122.42       0.48       0.22       0.14       0.16       0.15
##  [7]       0.06       0.84       0.04       0.53       0.07
##  [1] -391099.15       0.47       0.22       0.14       0.16       0.15
##  [7]       0.06       0.84       0.04       0.53       0.07
##  [1] -391078.99       0.47       0.22       0.14       0.17       0.15
##  [7]       0.05       0.84       0.04       0.53       0.07
##  [1] -391061.73       0.46       0.22       0.15       0.17       0.15
##  [7]       0.05       0.84       0.04       0.53       0.07
##  [1] -391047.15       0.45       0.23       0.15       0.18       0.15
##  [7]       0.05       0.84       0.04       0.53       0.07
##  [1] -391035.12       0.44       0.23       0.15       0.18       0.15
##  [7]       0.05       0.84       0.04       0.53       0.07
##  [1] -391025.34       0.43       0.23       0.15       0.19       0.15
##  [7]       0.05       0.84       0.04       0.53       0.07
## [1] 42
##  [1] "loglik"   "Prior(H)" "Prior(U)" "Prior(M)" "Prior(I)" "Mu(U)"   
##  [7] "Rho(U)"   "MU(M)"    "Rho(M)"   "mu_I"     "rho_I"   
##  [1] "XXX"  "0.41" "0.31" "0.27" "0.01" "0.1"  "0.1"  "0.9"  "0.03" "0.5" 
## [11] "0.05"
##  [1] -400462.75       0.57       0.25       0.16       0.02       0.15
##  [7]       0.07       0.87       0.03       0.51       0.05
##  [1] -393099.99       0.61       0.23       0.14       0.03       0.16
##  [7]       0.07       0.86       0.03       0.52       0.04
##  [1] -392431.12       0.62       0.22       0.12       0.03       0.16
##  [7]       0.07       0.85       0.03       0.52       0.04
##  [1] -392211.50       0.63       0.21       0.12       0.04       0.16
##  [7]       0.07       0.85       0.04       0.53       0.04
##  [1] -392110.42       0.63       0.21       0.12       0.04       0.16
##  [7]       0.07       0.85       0.04       0.53       0.04
##  [1] -392057.18       0.63       0.21       0.11       0.05       0.16
##  [7]       0.07       0.84       0.04       0.53       0.04
##  [1] -392025.77       0.63       0.20       0.11       0.05       0.16
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -392003.93       0.63       0.20       0.11       0.06       0.16
##  [7]       0.07       0.84       0.04       0.54       0.04
##  [1] -391983.17       0.62       0.20       0.11       0.06       0.16
##  [7]       0.06       0.84       0.04       0.54       0.04
##  [1] -391959.17       0.62       0.20       0.12       0.07       0.16
##  [7]       0.06       0.84       0.04       0.54       0.04
##  [1] -391929.79       0.61       0.20       0.12       0.07       0.15
##  [7]       0.06       0.84       0.04       0.54       0.04
##  [1] -391894.34       0.60       0.20       0.12       0.08       0.15
##  [7]       0.06       0.84       0.04       0.54       0.04
##  [1] -391853.10       0.60       0.20       0.12       0.08       0.15
##  [7]       0.06       0.84       0.04       0.54       0.05
##  [1] -391807.07       0.59       0.20       0.12       0.09       0.15
##  [7]       0.06       0.84       0.04       0.54       0.05
##  [1] -391757.19       0.59       0.20       0.12       0.09       0.15
##  [7]       0.06       0.84       0.04       0.54       0.05
##  [1] -391705.00       0.58       0.21       0.12       0.09       0.15
##  [7]       0.06       0.84       0.04       0.54       0.05
##  [1] -391651.85       0.57       0.21       0.12       0.10       0.15
##  [7]       0.06       0.84       0.04       0.54       0.05
##  [1] -391599.12       0.57       0.21       0.12       0.10       0.15
##  [7]       0.06       0.84       0.04       0.54       0.05
##  [1] -391547.56       0.56       0.21       0.13       0.11       0.15
##  [7]       0.06       0.84       0.04       0.54       0.06
##  [1] -391498.05       0.55       0.21       0.13       0.11       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391451.20       0.55       0.21       0.13       0.12       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391407.43       0.54       0.21       0.13       0.12       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391366.98       0.53       0.21       0.13       0.12       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391329.96       0.52       0.21       0.13       0.13       0.15
##  [7]       0.06       0.84       0.04       0.53       0.06
##  [1] -391296.39       0.52       0.22       0.13       0.13       0.15
##  [7]       0.06       0.84       0.04       0.53       0.07
##  [1] -391266.20       0.51       0.22       0.13       0.14       0.15
##  [7]       0.06       0.84       0.04       0.53       0.07
##  [1] -391239.26       0.50       0.22       0.14       0.14       0.15
##  [7]       0.06       0.84       0.04       0.53       0.07
##  [1] -391215.42       0.49       0.22       0.14       0.15       0.14
##  [7]       0.05       0.84       0.04       0.53       0.07
##  [1] -391194.51       0.49       0.22       0.14       0.15       0.14
##  [7]       0.05       0.84       0.04       0.52       0.07
##  [1] -391176.35       0.48       0.22       0.14       0.16       0.14
##  [7]       0.05       0.84       0.04       0.52       0.07
##  [1] -391160.74       0.47       0.22       0.14       0.16       0.14
##  [7]       0.05       0.84       0.04       0.52       0.07
##  [1] -391147.52       0.46       0.22       0.14       0.17       0.14
##  [7]       0.05       0.84       0.04       0.52       0.08
##  [1] -391136.51       0.46       0.23       0.14       0.17       0.14
##  [7]       0.05       0.84       0.04       0.52       0.08
##  [1] -391127.60       0.45       0.23       0.15       0.18       0.14
##  [7]       0.05       0.84       0.04       0.52       0.08
plts_paired_order<-plts_paired[order(validation_epic.organoid$passage)]

pdf(here("figs","validation_organoids_thresholding_all_samples.pdf"))
plts_paired_order
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dev.off()
## png 
##   2
###############

Differential methylation with passage

###############

Only in UT UD

validation_epic.organoid_UT_UD<-validation_epic.organoid[which(validation_epic.organoid$differentiation=="UD" & validation_epic.organoid$treatment=="UT"),]
table(validation_epic.organoid_UT_UD$passage_hilo)
## 
## high  low 
##    9    9
validation_organoid_beta_UT_UD<-validation_organoid_beta[,which(colnames(validation_organoid_beta)%in%validation_epic.organoid_UT_UD$array.id)]
identical(validation_epic.organoid_UT_UD$array.id, colnames(validation_organoid_beta_UT_UD))
## [1] TRUE
mod<-model.matrix(~ 0 + passage + individual, data=validation_epic.organoid_UT_UD)
fit <- lmFit(validation_organoid_beta_UT_UD, mod)
ebfit <- eBayes(fit)

# covariate adjusted beta values
passage_db<-sapply(1:nrow(validation_organoid_beta), function(x){
  sampleinfo_cpg<-validation_epic.organoid
  sampleinfo_cpg$beta<-as.numeric(validation_organoid_beta[x,])

  fit<-lm(beta ~ passage + individual, data=sampleinfo_cpg)
  pval<-summary(fit)$coef["passage","Pr(>|t|)"]
  slope<-fit$coefficients[2]

  (min(validation_epic.organoid$passage)*slope) - (max(validation_epic.organoid$passage)*slope)})

passage_validation<-data.frame(p.value=ebfit$p.value[,"passage"], CpG=rownames(validation_organoid_beta), db=passage_db)

# Adjust P values
passage_validation$p_adjusted<-p.adjust(passage_validation$p.value, method="BH")

diff_CpG_dbvalidation<-passage_validation[which(passage_validation$p_adjusted<0.05 & abs(passage_validation$db)>0.15),] #19746
diff_CpG_db_hypovalidation<-diff_CpG_dbvalidation$CpG[which((diff_CpG_dbvalidation$db)>=0.15)] #  19221
diff_CpG_db_hypervalidation<-diff_CpG_dbvalidation$CpG[which((diff_CpG_dbvalidation$db)<=(-0.15))] #  525

load original organoid passage CpGs

load(here("data","beta_organoids.RData"))
pvals_long<-read.csv(here("data","Heteroskedactiy_pvalues_FDR_1000iter.csv"), header=T)
pvals_long[,1]<-NULL
colnames(pvals_long)<-c("BP_count","diff_count","mean_db","fdr_BP","fdr_diff")
pvals_long$CpG<-rownames(organoid_beta)
pvals_long$BP_pval<-((1000-pvals_long$BP_count)+1)/1001
pvals_long$diff_pval<-((1000-pvals_long$diff_count)+1)/1001
pvals_long$BP_fdr<-((1000-pvals_long$fdr_BP)+1)/1001
pvals_long$diff_fdr<-((1000-pvals_long$fdr_diff)+1)/1001

hetero_CpG<-rownames(organoid_beta)[which(pvals_long$BP_fdr<0.05)]
print(paste("CpGs with significant (adjusted p<0.05) heteroskedactiy: ", length(hetero_CpG), sep=""))
## [1] "CpGs with significant (adjusted p<0.05) heteroskedactiy: 41852"
diff_CpG<-rownames(organoid_beta)[which(pvals_long$diff_fdr<0.05)]
diff_CpG_db<-pvals_long[which(pvals_long$diff_fdr<0.05 & abs(pvals_long$mean_db)>0.15),]
print(paste("CpGs with significant (adjusted p<0.05; delta beta >0.05) differential methylation: ", nrow(diff_CpG_db), sep=""))
## [1] "CpGs with significant (adjusted p<0.05; delta beta >0.05) differential methylation: 23766"
diff_CpG_db_hypo<-diff_CpG_db$CpG[which((diff_CpG_db$mean_db)>=0.15)] #  11772
diff_CpG_db_hyper<-diff_CpG_db$CpG[which((diff_CpG_db$mean_db)<=(-0.15))] #  5214

How many differential CpGs could overlap? 450K vs EPIC

print(paste("Of the ", nrow(diff_CpG_db), " CpGs differential with passage in the original organoids, ",
            length(diff_CpG_db$CpG[which(diff_CpG_db$CpG%in%rownames(validation_organoid_beta))]), " are in the validation data", sep=""))
## [1] "Of the 23766 CpGs differential with passage in the original organoids, 23737 are in the validation data"
diff_CpG_db_hypo_overlap<-diff_CpG_db_hypo[which(diff_CpG_db_hypo%in%rownames(validation_organoid_beta))]
diff_CpG_db_hyper_overlap<-diff_CpG_db_hyper[which(diff_CpG_db_hyper%in%rownames(validation_organoid_beta))]

diff_CpG_db_hypovalidation_overlap<-diff_CpG_db_hypovalidation[which(diff_CpG_db_hypovalidation%in%pvals_long$CpG)]
diff_CpG_db_hypervalidation_overlap<-diff_CpG_db_hypervalidation[which(diff_CpG_db_hypervalidation%in%pvals_long$CpG)]

print(paste("Of the ",length(diff_CpG_db_hypo_overlap)," hypo CpGs also on the 450K ",
            length(intersect(diff_CpG_db_hypovalidation_overlap, diff_CpG_db_hypo_overlap))," are also hypo in the validation cohort (",
            round((length(intersect(diff_CpG_db_hypovalidation_overlap, diff_CpG_db_hypo_overlap))/length(diff_CpG_db_hypo_overlap))*100,2),"%)",sep=""))
## [1] "Of the 17327 hypo CpGs also on the 450K 9349 are also hypo in the validation cohort (53.96%)"
print(paste("Of the ",length(diff_CpG_db_hyper_overlap)," hypo CpGs also on the 450K ",
            length(intersect(diff_CpG_db_hypervalidation_overlap, diff_CpG_db_hyper_overlap))," are also hypo in the validation cohort (",
            round((length(intersect(diff_CpG_db_hypervalidation_overlap, diff_CpG_db_hyper_overlap))/length(diff_CpG_db_hyper_overlap))*100,2),"%)",sep=""))
## [1] "Of the 6410 hypo CpGs also on the 450K 457 are also hypo in the validation cohort (7.13%)"

delta beta directionality plot

plt_db_direction<-merge(pvals_long[,c(3,6)], passage_validation, by="CpG")# 380776

plt_db_direction$sig<-"Not Significant"
plt_db_direction$sig[which(plt_db_direction$CpG%in%c(intersect(diff_CpG_db_hypovalidation_overlap, diff_CpG_db_hypo_overlap),intersect(diff_CpG_db_hypervalidation_overlap, diff_CpG_db_hyper_overlap)))]<-"Significant\nIn Both\nCohorts"

ggplot(plt_db_direction, aes(mean_db, db))+geom_point(aes(color=sig, alpha=sig),shape=19)+th+theme_bw()+
  scale_color_manual(values=c("lightgrey", "cornflowerblue"), name="Significant\nWith Passage")+
  scale_alpha_manual(values=c(0.25,1), guide=F)+
  geom_hline(yintercept=c(-0.15,0.15), color="grey60")+geom_vline(xintercept=c(-0.15,0.15), color="grey60")+
  ylim(-0.9,0.9)+xlim(-0.9,0.9)+xlab("Cohort 1 Organoid\nPassage Delta Beta")+ylab("Validation Organoid\nPassage Delta Beta")+
  stat_smooth(method="lm", se=F, color="black")

#ggsave(here("figs","validation_db_directionality.pdf"), width=5, height=3.75)
ggsave(here("figs/jpeg","validation_db_directionality.jpeg"), width=5, height=3.75)

print(paste("Correlation of delta betas between cohorts: ", round(cor(plt_db_direction$db, plt_db_direction$mean_db),2), sep=""))
## [1] "Correlation of delta betas between cohorts: 0.67"

representative CpGs

epic.organoid_minimal<-epic.organoid[,c(2, 14, 17)]
colnames(epic.organoid_minimal)[1]<-"Assay.Name"
epic.organoid_minimal$cohort<-"Cohort 1 Organoids"

validation_epic.organoid_UT_UD$Sample_ID<-paste(validation_epic.organoid_UT_UD$individual, validation_epic.organoid_UT_UD$Segment, validation_epic.organoid_UT_UD$condition)
validation_epic.organoid_minimal<-validation_epic.organoid_UT_UD[,c(10, 19, 12)]
colnames(validation_epic.organoid_minimal)[1]<-"Assay.Name"
validation_epic.organoid_minimal$cohort<-"Validation Organoids"
colnames(validation_epic.organoid_minimal)[2:3]<-c("sample_ID","passage.or.rescope.no_numeric")

sample_info_both<-rbind(validation_epic.organoid_minimal,epic.organoid_minimal)
sample_info_both$passage.or.rescope.no_numeric<-as.numeric(as.character(sample_info_both$passage.or.rescope.no_numeric))

plt_hetero_validation<-function(CpGs, legend, axislab, title){
  betas<-melt(cbind(validation_organoid_beta_UT_UD[CpGs,],organoid_beta[CpGs,]))
  organoid_plt<-merge(sample_info_both, betas, by.x="Assay.Name",by.y="Var2")

  p<-ggplot(organoid_plt, aes(passage.or.rescope.no_numeric,value))+
    geom_line(aes(group=sample_ID),color="lightgrey")+
    stat_smooth(method="lm", color="grey30", size=0.7, se=F)+th+theme_bw()+
    geom_point(aes(fill=as.factor(passage.or.rescope.no_numeric)),shape=21, size=1.25)+
    scale_fill_manual(values=pass_col,name="Passage\nNumber", drop=T)+
    facet_grid(cohort~Var1)+
    ylab("DNAm Beta")+xlab("Passage Number")+ylim(0,1)+
    theme(plot.margin = margin(0.5, 0.15, 0.5, 0.15, "cm"),plot.title = element_text(size=12))+
    xlim(1,16)

  if(missing(legend) & missing(axislab) & missing(title)){p}else{
    if(legend=="N" & axislab=="N"){p + theme(legend.position = "none",axis.title.y=element_blank(),
                                             axis.text.y=element_blank(),
                                             axis.ticks.y=element_blank())+ ggtitle(title)}else{
                                               if(legend=="N" & axislab=="Y"){p + theme(legend.position = "none") + ggtitle(title)}}}}

plt_hetero_validation(c("cg25402228","cg22009751"))
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## Warning: Removed 10 rows containing missing values (geom_smooth).

ggsave(here("figs","Passage_differential_CpGs_validation.pdf"),width = 4.75, height = 4)
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## Warning: Removed 10 rows containing missing values (geom_smooth).
ggsave(here("figs/jpeg","Passage_differential_CpGs_validation.jpeg"), width = 4.75, height = 4)
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## Warning: Removed 10 rows containing missing values (geom_smooth).

CpG to gene associations

EPIC_genes<-read.csv(here("data","EPIC_ensembl_gene_annotation.csv")) # 1137194

diff_genes_db_hypovalidation<-unique(EPIC_genes$Gene.name[which(EPIC_genes$IlmnID%in%diff_CpG_db_hypovalidation)] ) #8365
diff_genes_db_hypervalidation<-unique(EPIC_genes$Gene.name[which(EPIC_genes$IlmnID%in%diff_CpG_db_hypervalidation)] ) # 454

write.table(diff_genes_db_hypovalidation, file=here("data/validation/DNAm/","validation_genes_hypomethylation_UTUD.txt"), quote=F, row.names = F, col.names = F)
write.table(diff_genes_db_hypervalidation, file=here("data/validation/DNAm/","validation_genes_hypermethylation_UTUD.txt"), quote=F, row.names = F, col.names = F)

Genes differential in original and validation

diff_genes_db_hypovalidation_original<-unique(EPIC_genes$Gene.name[which(EPIC_genes$IlmnID%in%intersect(diff_CpG_db_hypovalidation_overlap, diff_CpG_db_hypo_overlap))] ) # 4722
diff_genes_db_hypervalidation_original<-unique(EPIC_genes$Gene.name[which(EPIC_genes$IlmnID%in%intersect(diff_CpG_db_hypervalidation_overlap, diff_CpG_db_hyper_overlap))] ) # 402
write.table(diff_genes_db_hypovalidation_original, file=here("data/validation/DNAm/","validation_original_genes_hypomethylation_UTUD.txt"), quote=F, row.names = F, col.names = F)
write.table(diff_genes_db_hypervalidation_original, file=here("data/validation/DNAm/","validation_original_genes_hypermethylation_UTUD.txt"), quote=F, row.names = F, col.names = F)

DNAm plot of differenitally expressed genes

gene_DNAm<-function(gene){
  CpG_goi<-EPIC_genes[which(EPIC_genes$Gene.name%in%gene),]
  CpG_gene<-CpG_goi[which(CpG_goi$IlmnID%in%c(diff_CpG_db_hypovalidation_overlap, diff_CpG_db_hypervalidation_overlap)),]
  CpGs<-unique(CpG_gene$IlmnID)
  
  CpG_gene<-CpG_gene[!duplicated(CpG_gene[,c(3,7)]), c(3,7)]
  CpG_gene$label<-paste(CpG_gene$IlmnID, "\n(",CpG_gene$Gene.name, ")", sep="")
  
  betas<-melt(cbind(validation_organoid_beta_UT_UD[CpGs,],organoid_beta[CpGs,]))
  organoid_plt<-merge(sample_info_both, betas, by.x="Assay.Name",by.y="Var2")
  organoid_plt<-merge(organoid_plt, CpG_gene, by.x="Var1",by.y="IlmnID")
  
  ggplot(organoid_plt, aes(passage.or.rescope.no_numeric,value))+
    geom_line(aes(group=sample_ID),color="lightgrey")+
    stat_smooth(method="lm", color="grey30", size=0.7, se=F)+th+theme_bw()+
    geom_point(aes(fill=as.factor(passage.or.rescope.no_numeric)),shape=21, size=1.25)+
    scale_fill_manual(values=pass_col,name="Passage\nNumber", drop=T)+
    facet_grid(cohort~label)+
    ylab("DNAm Beta")+xlab("Passage Number")+ylim(0,1)+
    theme(plot.margin = margin(0.5, 0.15, 0.5, 0.15, "cm"),plot.title = element_text(size=12))+
    xlim(1,16)
  }

gene_DNAm(c("EDAR","RNASE4","EIF4G1","LRRC59"))
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?

ggsave(here("figs","validation_differenital_DNAm_passage.pdf"),width = 9, height = 4)
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
ggsave(here("figs/jpeg","validation_differenital_DNAm_passage.jpeg"), width = 9, height = 4)
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to
## adjust the group aesthetic?

R Session Info

sessionInfo()
## R version 3.5.1 (2018-07-02)
## Platform: x86_64-conda_cos6-linux-gnu (64-bit)
## Running under: Red Hat Enterprise Linux Server 7.4 (Maipo)
## 
## Matrix products: default
## BLAS/LAPACK: /homes/redgar/anaconda3/envs/org_pass/lib/R/lib/libRblas.so
## 
## locale:
##  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
##  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
##  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
##  [1] splines   stats4    parallel  stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
##  [2] IlluminaHumanMethylationEPICmanifest_0.3.0         
##  [3] VGAM_1.1-1                                         
##  [4] reshape2_1.4.3                                     
##  [5] scales_1.0.0                                       
##  [6] rafalib_1.0.0                                      
##  [7] gtools_3.8.1                                       
##  [8] lmtest_0.9-37                                      
##  [9] zoo_1.8-4                                          
## [10] dplyr_0.8.0.1                                      
## [11] GEOmetadb_1.44.0                                   
## [12] RSQLite_2.1.1                                      
## [13] GEOquery_2.50.0                                    
## [14] pamr_1.56                                          
## [15] survival_2.43-3                                    
## [16] cluster_2.0.7-1                                    
## [17] sva_3.30.0                                         
## [18] genefilter_1.64.0                                  
## [19] mgcv_1.8-26                                        
## [20] nlme_3.1-137                                       
## [21] limma_3.38.3                                       
## [22] binom_1.1-1                                        
## [23] here_0.1                                           
## [24] RColorBrewer_1.1-2                                 
## [25] gridExtra_2.3                                      
## [26] ggplot2_3.1.0                                      
## [27] reshape_0.8.8                                      
## [28] minfi_1.28.0                                       
## [29] bumphunter_1.24.5                                  
## [30] locfit_1.5-9.1                                     
## [31] iterators_1.0.10                                   
## [32] foreach_1.4.4                                      
## [33] Biostrings_2.50.1                                  
## [34] XVector_0.22.0                                     
## [35] SummarizedExperiment_1.12.0                        
## [36] DelayedArray_0.8.0                                 
## [37] BiocParallel_1.16.2                                
## [38] matrixStats_0.54.0                                 
## [39] Biobase_2.42.0                                     
## [40] GenomicRanges_1.34.0                               
## [41] GenomeInfoDb_1.18.1                                
## [42] IRanges_2.16.0                                     
## [43] S4Vectors_0.20.1                                   
## [44] BiocGenerics_0.28.0                                
## 
## loaded via a namespace (and not attached):
##  [1] colorspace_1.4-0         siggenes_1.56.0         
##  [3] mclust_5.4.2             rprojroot_1.3-2         
##  [5] base64_2.0               bit64_0.9-7             
##  [7] AnnotationDbi_1.44.0     xml2_1.2.0              
##  [9] codetools_0.2-16         knitr_1.21              
## [11] Rsamtools_1.34.0         annotate_1.60.0         
## [13] HDF5Array_1.10.1         readr_1.3.1             
## [15] compiler_3.5.1           httr_1.4.0              
## [17] backports_1.1.3          assertthat_0.2.0        
## [19] Matrix_1.2-15            lazyeval_0.2.1          
## [21] htmltools_0.3.6          prettyunits_1.0.2       
## [23] tools_3.5.1              gtable_0.2.0            
## [25] glue_1.3.0               GenomeInfoDbData_1.2.0  
## [27] doRNG_1.7.1              Rcpp_1.0.0              
## [29] multtest_2.38.0          preprocessCore_1.44.0   
## [31] rtracklayer_1.42.2       DelayedMatrixStats_1.4.0
## [33] xfun_0.4                 stringr_1.4.0           
## [35] rngtools_1.3.1           XML_3.98-1.16           
## [37] beanplot_1.2             zlibbioc_1.28.0         
## [39] MASS_7.3-51.1            hms_0.4.2               
## [41] rhdf5_2.26.2             yaml_2.2.0              
## [43] memoise_1.1.0            pkgmaker_0.27           
## [45] biomaRt_2.38.0           stringi_1.2.4           
## [47] highr_0.7                GenomicFeatures_1.34.1  
## [49] bibtex_0.4.2             rlang_0.3.1             
## [51] pkgconfig_2.0.2          bitops_1.0-6            
## [53] nor1mix_1.2-3            evaluate_0.12           
## [55] lattice_0.20-38          purrr_0.2.5             
## [57] Rhdf5lib_1.4.2           labeling_0.3            
## [59] GenomicAlignments_1.18.0 bit_1.1-12              
## [61] tidyselect_0.2.5         plyr_1.8.4              
## [63] magrittr_1.5             R6_2.4.0                
## [65] DBI_1.0.0                pillar_1.4.3            
## [67] withr_2.1.2              RCurl_1.95-4.11         
## [69] tibble_2.0.1             crayon_1.3.4            
## [71] rmarkdown_1.11           progress_1.2.0          
## [73] grid_3.5.1               data.table_1.12.0       
## [75] blob_1.1.1               digest_0.6.18           
## [77] xtable_1.8-2             tidyr_0.8.2             
## [79] illuminaio_0.24.0        openssl_1.1             
## [81] munsell_0.5.0            registry_0.5            
## [83] quadprog_1.5-5